Dynamics of chromosome organization in a minimal bacterial cell
Open accessAbstract
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics, we investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell-cycle. To achieve cell-scale chromosome structures that are realistic, we model the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. In addition, the conformations of the circular DNA must avoid overlapping with ribosomes identitied in cryo-electron tomograms. While Syn3A lacks the complex regulatory systems known to orchestrate chromosome segregation in other bacteria, its minimized genome retains essential loop-extruding structural maintenance of chromosomes (SMC) protein complexes (SMC-scpAB) and topoisomerases. Through implementing the effects of these proteins in our simulations of replicating chromosomes, we find that they alone are sufficient for simultaneous chromosome segregation across all generations within nested theta structures. This supports previous studies suggesting loop-extrusion serves as a near-universal mechanism for chromosome organization within bacterial and eukaryotic cells. Furthermore, we analyze ribosome diffusion under the influence of the chromosome and calculate in silico chromosome contact maps that capture inter-daughter interactions. Finally, we present a methodology to map the polymer model of the chromosome to a Martini coarse-grained representation to prepare molecular dynamics models of entire Syn3A cells, which serves as an ultimate means of validation for cell states predicted by the WCM.
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At the finest level of resolution, a near-atomic structure of JCVI-syn3A has been modeled using the coarse-grained Martini force field.
“At the finest level of resolution, a near-atomic structure of a minimal bacterium (JCVI-syn3A) has been modeled using the coarse-grained Martini force field.”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [7]
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“Based on these results in other bacteria and HU ’ s enhanced binding to dsDNA repair and recombination intermediates (Kamashev, 2000), we believe a small number of HU was retained to ful fi ll an essential role during replication initiation using a DnaA-based oriC in Syn3A (Thornburg et al., 2019),…”
Physical manipulation of the Escherichia coli chromosome reveals its soft nature
Pelletier, J. F., Halvorsen, K., Ha, B., Paparcone, R., Sandler, S. J., Woldringh, C., Wong, W. P., & Jun, S. (2012) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1208689109 · Cited by 200 · see citing works
Essential metabolism for a minimal cell
Breuer, M., Earnest, E. E., Merryman, C., Wise, K. S., Sun, L., Lynott, M. R., Hutchison, C. A., Smith, H. O., Lapek, J. D., Gonzalez, D. J., et al. (2019) · eLife · doi:10.7554/elife.36842 · Cited by 190 · cited 10× · see citing works
“…that both DNA-looping and strand-crossings are necessary for the segregation of daughter chromosomes during and after replication, which is in agreement with Syn3A ′ s gene essentiality data for SMC-complexes and type-II topoisomerases from transposon mutagenesis experiments (Breuer et al., 2019).”
InfluentialSelf-citationVisualizing translation dynamics at atomic detail inside a bacterial cell
Xue, L., Lenz, S., Zimmermann-Kogadeeva, M., Tegunov, D., Cramer, P., Bork, P., Rappsilber, J., & Mahamid, J. (2022) · Nature · doi:10.1038/s41586-022-05255-2 · Cited by 184 · cited 2× · see citing works
“In the case of the ribosomes, their characteristic size is 20 nm when we do not include polysomes (multiple ribosomes translating a single mRNA) (Xue et al., 2022), and their motion should be decoupled from metabolic activity due to falling below a 30 nm size threshold (Parry et al., 2014).”
Anomalous Diffusion: A Basic Mechanism for the Evolution of Inhomogeneous Systems
Oliveira, F. A., Ferreira, R. M. S., Lapas, L. C., & Vainstein, M. H. (2019) · Frontiers in Physics · doi:10.3389/fphy.2019.00018 · Cited by 181 · see citing works
Sanamrad, A., Persson, F., Lundius, E. G., Fange, D., Gynnå, A. H., & Elf, J. (2014) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1411558111 · Cited by 177 · cited 1× · see citing works
“The Brownian diffusion constants of ribosomes in systems with bonds is within the range of experimental measurements in other bacteria (Bakshi et al., 2012; Sanamrad et al., 2014).”
Measurement of the torque on a single stretched and twisted DNA using magnetic tweezers.
Mosconi, F., Allemand, J., Bensimon, D., & Croquette, V. (2009) · Physical Review Letters · doi:10.1103/physrevlett.102.078301 · Cited by 175
Progressive segregation of the Escherichia coli chromosome
Nielsen, H. J., Li, Y., Youngren, B., Hansen, F., & Austin, S. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05245.x · Cited by 167
Fundamental behaviors emerge from simulations of a living minimal cell
Thornburg, Z. R., Bianchi, D. M., Brier, T. A., Gilbert, B. R., Earnest, E. E., Melo, M. C. R., Safronova, N., Sáenz, J. P., Cook, A. T., Wise, K. S., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.025 · Cited by 165 · see citing works
Self-citationPolyply; a python suite for facilitating simulations of macromolecules and nanomaterials
Grünewald, F., Alessandri, R., Kroon, P. C., Monticelli, L., Souza, P. C. T., & Marrink, S. (2021) · Nature Communications · doi:10.1038/s41467-021-27627-4 · Cited by 157 · see citing works
Self-citationMolecular dynamics simulation of an entire cell
Stevens, J. A., Grünewald, F., van Tilburg, P. A. M., König, M., Gilbert, B. R., Brier, T. A., Thornburg, Z. R., Luthey-Schulten, Z., & Marrink, S. J. (2023) · Frontiers in Chemistry · doi:10.3389/fchem.2023.1106495 · Cited by 156 · cited 2× · see citing works
“Researchers have previously completed molecular dynamics (MD) simulations of representative volumes of bacterial cytoplasm (Yu et al., 2016; Rickard et al., 2019; Heo et al., 2022), but only recently has it become possible to prepare a MD simulation of an entire bacterium (Stevens et al., 2023).”
Self-citationStructure of Full-Length SMC and Rearrangements Required for Chromosome Organization
Diebold-Durand, M.-L., Lee, H., Ruiz-Ávila, L. B., Noh, H., Shin, H.-C., Im, H., Bock, F., Burmann, F., Durand, A., Basfeld, A., et al. (2017) · Molecules and Cells · doi:10.1016/j.molcel.2017.06.010 · Cited by 155 · see citing works
Simultaneous cross-evaluation of heterogeneous <i>E. coli</i> datasets via mechanistic simulation
Macklin, D. N., Ahn-Horst, T. A., Choi, H., Ruggero, N. A., Carrera, J., Mason, J. C., Sun, G., Agmon, E., DeFelice, M. M., Maayan, I., et al. (2020) · Science · doi:10.1126/science.aav3751 · Cited by 151 · cited 1× · see citing works
“…where the propagation is governed by the chemical and physical interactions within the cell and between the cell and its environment (Karr et al., 2012; Goldberg et al., 2018; Macklin et al., 2020; Marucci et al., 2020; Luthey-Schulten et al., 2022; Maritan et al., 2022; Thornburg et al., 2022).”
Chromosome organization by one-sided and two-sided loop extrusion
Banigan, E. J., van den Berg, A. A., Brandão, H. B., Marko, J. F., & Mirny, L. A. (2020) · eLife · doi:10.7554/elife.53558 · Cited by 146 · cited 1× · see citing works
“…Giorgetti, 2019) are required to solve the inverse problem of determining 3D genome organization (Di Pierro et al., 2017; Messelink et al., 2021; Shi and Thirumalai, 2023) and provide mechanistic insights (Sanborn et al., 2015; Fudenberg et al., 2016; Banigan et al., 2020; Fiorillo et al., 2021).”
DNA-loop extruding condensin complexes can traverse one another
Kim, E., Kerssemakers, J., Shaltiel, I. A., Haering, C., & Dekker, C. (2019) · Nature · doi:10.1038/s41586-020-2067-5 · Cited by 145 · cited 1× · see citing works
“Based on results showing that eukaryotic SMC complexes can traverse one-another to form Z-loops (Kim et al., 2020), we do not include any interactions between hinge and anchors that are not paired.”
Klenin, K., Merlitz, H., & Langowski, J. (1998) · Biophysical Journal · doi:10.1016/s0006-3495(98)74003-2 · Cited by 142
Temperature dependence of DNA persistence length
Geggier, S., Kotlyar, A., & Vologodskii, A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq932 · Cited by 141 · cited 2× · see citing works
“The linear and torsional stiffness parameters, κ b and κ t , are determined based on the assumed linear persistence length, l p , of 45 nm (Manning, 2006; Geggier et al., 2010; Mantelli et al., 2011) and twist persistence length, l t , of 85 nm (Mosconi et al., 2009), respectively.”
Modulation of Escherichia coli sister chromosome cohesion by topoisomerase IV.Preprint
Wang, X., Reyes-Lamothe, R., & Sherratt, D. (2008) · Genes & Development · doi:10.1101/gad.487508 · Cited by 137 · see citing works
Architecture of the Escherichia coli nucleoid
Verma, S., Qian, Z., & Adhya, S. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008456 · Cited by 132 · cited 1× · see citing works
“…study (Gilbert et al., 2021), unlike many bacteria Syn3A codes for a single nucleoid-associated protein (NAP) (Dame, 2005; Lioy et al., 2018; Verma et al., 2019; Lioy et al., 2021), HU (JCVISYN3A_0350), which is known to have two binding modes: 1) low-af fi nity binding to linear DNA and 2)…”
Closing the loop: 3C versus DNA FISH
Giorgetti, L., & Heard, E. (2016) · Genome Biology · doi:10.1186/s13059-016-1081-2 · Cited by 131 · cited 2× · see citing works
“While imaging techniques such as DNA-FISH (Giorgetti and Heard, 2016) provide insights about targeted interactions, the wide-spread accessibility of next-generation sequencing (Goodwin et al., 2016) catalyzed the proliferation of sequence-based techniques that assess genome-wide interactions such as DNA-protein bindin…”
Backmapping triangulated surfaces to coarse-grained membrane models
Pezeshkian, W., König, M., Wassenaar, T., & Marrink, S. (2020) · Nature Communications · doi:10.1038/s41467-020-16094-y · Cited by 129 · see citing works
Self-citationTran, N., Laub, M., & Le, T. (2017) · bioRxiv · doi:10.1101/125344 · Cited by 125 · see citing works
Youngren, B., Nielsen, H. J., Jun, S., & Austin, S. (2014) · Genes & Development · doi:10.1101/gad.231050.113 · Cited by 122
DNA supercoiling and transcription in bacteria: a two-way street
Dorman, C. (2019) · BMC Molecular and Cell Biology · doi:10.1186/s12860-019-0211-6 · Cited by 118 · cited 1× · see citing works
“…(Lioy et al., 2018) when its expression is restored and to mechanochemically couple transcriptional activity in the 4D-WCM to the torsional state of the chromosome (Liu and Wang, 1987; Chong et al., 2014; Dorman, 2019; Kim et al., 2019; Chatterjee et al., 2021; Guo et al., 2021; Geng et al., 2022).”
Roberts, E., Stone, J. E., & Luthey‐Schulten, Z. (2013) · Journal of Computational Chemistry · doi:10.1002/jcc.23130 · Cited by 117 · cited 1× · see citing works
“By combining these with hybrid stochastic-deterministic methods leveraging GPU-accelerated simulation software (Roberts et al., 2012; Hallock et al., 2014; Bianchi et al., 2018), a well-stirred WCM (WS-WCM) and 3D spatially resolved WCM (4D-WCM) that predict time-dependent Syn3A cell states were…”
Self-citationBidirectional chromosome replication: some topological considerations.
Dingman, C. (1974) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(74)80052-4 · Cited by 117 · cited 1×
“In the “ train-track ” model of bacterial DNA replication (Gogou et al., 2021), the replisomes are thought to independently traverse the opposite arms of the mother chromosome while replicating the DNA (Dingman, 1974).”
Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae
Trussart, M., Yus, E., Martinez, S., Baù, D., Tahara, Y. O., Pengo, T., Widjaja, M., Kretschmer, S., Swoger, J., Djordjevic, S., et al. (2017) · Nature Communications · doi:10.1038/ncomms14665 · Cited by 114 · see citing works
Introducing Memory in Coarse-Grained Molecular Simulations
Klippenstein, V., Tripathy, M., Jung, G., Schmid, F., & van der Vegt, N. F. A. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.1c01120 · Cited by 112 · see citing works
MatP regulates the coordinated action of topoisomerase IV and MukBEF in chromosome segregation
Nolivos, S., Upton, A. L., Badrinarayanan, A., Müller, J., Zawadzka, K., Wiktor, J., Gill, A., Arciszewska, L., Nicolas, E., & Sherratt, D. (2016) · Nature Communications · doi:10.1038/ncomms10466 · Cited by 112 · see citing works
‘Entropy-Based mechanism of ribosome-nucleoid segregation in E. coli cells’
Mondal, J., Bratton, B. P., Li, Y., Yethiraj, A., & Weisshaar, J. C. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.04.030 · Cited by 110 · cited 1× · see citing works
“Before we try to quantify how the effects of these coupled mechanisms affect the spatial organization and diffusion of the chromosome and ribosomes (Mondal et al., 2011), here we quantify how the chromosome and complete, intact ribosomes affect the diffusion of one another at the scale of a whole…”
SIRAH tools: mapping, backmapping and visualization of coarse-grained models
Machado, M. R., & Pantano, S. (2016) · Bioinform. · doi:10.1093/bioinformatics/btw020 · Cited by 107 · see citing works
Subdiffusive motion of a polymer composed of subdiffusive monomers
Weber, S. C., Theriot, J., & Spakowitz, A. (2010) · Physical review. E, Statistical, nonlinear, and soft matter physics · doi:10.1103/physreve.82.011913 · Cited by 107 · see citing works
Conformation of sister chromatids in the replicated human genome
Mitter, M., Gasser, C., Takács, Z., Langer, C. C. H., Tang, W., Jessberger, G., Beales, C. T., Neuner, E., Ameres, S. L., Peters, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2744-4 · Cited by 107 · see citing works
Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling
Kim, S., Beltran, B. G., Irnov, I., & Jacobs, C. (2019) · Cell · doi:10.1016/j.cell.2019.08.033 · Cited by 106 · cited 2× · see citing works
“…the absence of regulatory elements in Syn3A, an open-question is if the arrangement of genes can serve as a means of regulation (Chatterjee et al., 2021; Geng et al., 2022) as a result of the mechanochemical coupling between transcription and supercoiling (Chong et al., 2014; Kim et al., 2019).”
Zawadzki, P., Stracy, M., Ginda, K., Zawadzka, K., Lesterlin, C., Kapanidis, A., & Sherratt, D. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.11.034 · Cited by 105
MEDYAN: mechanochemical simulations of contraction and polarity alignment in actomyosin networks
Popov, K., Komianos, J., & Papoian, G. A. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004877 · Cited by 104 · cited 1× · see citing works
“Information concerning the spatial coordinates of the replicating genome will be sent to the 4D-WCM and information regarding reaction events will be returned, similar approaches have been used by other researchers (Popov et al., 2016).”
Objective comparison of methods to decode anomalous diffusion
Muñoz-Gil, G., Volpe, G., García-March, M., Aghion, E., Argun, A., Hong, C., Bland, T., Bo, S., Conejero, J. A., Firbas, N., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26320-w · Cited by 102 · see citing works
A Brownian ratchet model for DNA loop extrusion by the cohesin complex
Higashi, T. L., Tang, M., Pobegalov, G. E., Uhlmann, F., & Molodtsov, M. I. (2021) · eLife · doi:10.7554/elife.67530 · Cited by 95 · see citing works
Escherichia coli DnaA interacts with HU in initiation at the E. coli replication origin
Chodavarapu, S., Felczak, M. M., Yaniv, J. R., & Kaguni, J. (2007) · Molecular Microbiology · doi:10.1111/j.1365-2958.2007.06094.x · Cited by 94
Fractal and statistical properties of large compact polymers: a computational study
Lua, R., Borovinskiy, A. L., & Grosberg, A. (2003) · Polymer · doi:10.1016/j.polymer.2003.10.073 · Cited by 91 · cited 1× · see citing works
“…uses a series of decreasing cylinder lengths during the growth process to generate a chromosome con fi guration organized as a fractal globule (Lua et al., 2004) with clearly-de fi ned chromosomal territories (Lieberman-Aiden et al., 2009; Sanborn et al., 2015), which is consistent with our…”
Organization of the Escherichia coli Chromosome by a MukBEF Axial Core
Mäkelä, J., & Sherratt, D. (2020) · Molecules and Cells · doi:10.1016/j.molcel.2020.02.003 · Cited by 90 · cited 1× · see citing works
“This coordinated role between SMC complexes and topo-IV has been observed in E. coli (Zawadzki et al., 2015; Nolivos et al., 2016; Mäkelä and Sherratt, 2020).”
Ryu, J.-K., Rah, S.-H., Janissen, R., Kerssemakers, J. W. J., Bonato, A., Michieletto, D., & Dekker, C. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1268 · Cited by 87 · cited 7× · see citing works
“For this study we made the simplifying assumption that only intra-strand motion is permitted ( p unbind = 0), which has been used in other studies (Ryu et al., 2021), but the software is capable of simulating inter-strand motion.”
InfluentialHigh-resolution, genome-wide mapping of positive supercoiling in chromosomes
Guo, M. S., Kawamura, R., Littlehale, M. L., Marko, J., & Laub, M. (2021) · bioRxiv · doi:10.7554/elife.67236 · Cited by 85 · see citing works
Towards a synthetic cell cycle
Olivi, L., Berger, M., Creyghton, R., de Franceschi, N., Dekker, C., Mulder, B., Claassens, N., ten Wolde, P. T., & van der Oost, J. (2021) · Nature Communications · doi:10.1038/s41467-021-24772-8 · Cited by 84 · see citing works
MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems
Maffeo, C. M., & Aksimentiev, A. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa200 · Cited by 82 · cited 2× · see citing works
“Previous dynamics simulations of entire chromosomes are either based on simpli fi ed (1-2 bead per bp) models or are restricted to simulating smaller, viral genomes and nanostructures (Maffeo and Aksimentiev, 2020; Sengar et al., 2021).”
Emerging whole-cell modeling principles and methods
Goldberg, A. P., Szigeti, B., Yin, H.-C., Sekar, J. A. P., Roth, Y. D., & Karr, J. R. (2017) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2017.12.013 · Cited by 82 · see citing works
Brownian dynamics of confined rigid bodies.
Delong, S., Balboa-Usabiaga, F., & Donev, A. (2015) · Journal of Chemical Physics · doi:10.1063/1.4932062 · Cited by 82
Interconnecting solvent quality, transcription, and chromosome folding in Escherichia coli.
Xiang, Y., Surovtsev, I., Chang, Y.-J., Govers, S., Parry, B. R., Liu, J., & Jacobs-Wagner, C. (2021) · Cell · doi:10.1016/j.cell.2021.05.037 · Cited by 80 · cited 1× · see citing works
“…Material), we determined that this was a result of the system with bonds creating a polymer mesh with persistent voids (Sorichetti et al., 2020; Xiang et al., 2021) for the ribosomes to diffuse within, in contrast to the case without bonds where the DNA monomers rapidly diffuse and are closely…”
Intracellular ion concentrations and cation-dependent remodelling of bacterial MreB assemblies
Szatmári, D., Sárkány, P., Kocsis, B., Nagy, T., Miseta, A., Barkó, S., Longauer, B., Robinson, R., & Nyitrai, M. (2020) · Scientific Reports · doi:10.1038/s41598-020-68960-w · Cited by 76 · see citing works
Building structural models of a whole mycoplasma cell
Maritan, M., Autin, L., Karr, J., Covert, M. W., Olson, A. J., & Goodsell, D. S. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167351 · Cited by 75 · see citing works
Computational models of large-scale genome architecture.
Rosa, A., & Zimmer, C. (2014) · International Review of Cell and Molecular Biology · doi:10.1016/b978-0-12-800046-5.00009-6 · Cited by 74 · cited 1× · see citing works
“Although researchers have a stunning breadth of experimental data characterizing interactions throughout the genome, computational models (Rosa and Zimmer, 2014; Tiana and Giorgetti, 2019) are required to solve the inverse problem of determining 3D genome organization (Di Pierro et al., 2017;…”
Mantelli, S., Muller, P., Harlepp, S., & Maaloum, M. (2011) · Soft Matter · doi:10.1039/c0sm01160f · Cited by 73 · see citing works
Sister chromatid interactions in bacteria revealed by a site‐specific recombination assay
Lesterlin, C., Gigant, E., Boccard, F., & Espéli, O. (2012) · EMBO Journal · doi:10.1038/emboj.2012.194 · Cited by 71 · see citing works
Sengar, A., Ouldridge, T., Henrich, O., Rovigatti, L., & Šulc, P. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.693710 · Cited by 70 · see citing works
Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin
Fiorillo, L., Musella, F., Conte, M., Kempfer, R., Chiariello, A. M., Bianco, S., Kukalev, A., Irastorza-Azcárate, I., Esposito, A., Abraham, A., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01135-1 · Cited by 68 · cited 1× · see citing works
“…Giorgetti, 2019) are required to solve the inverse problem of determining 3D genome organization (Di Pierro et al., 2017; Messelink et al., 2021; Shi and Thirumalai, 2023) and provide mechanistic insights (Sanborn et al., 2015; Fudenberg et al., 2016; Banigan et al., 2020; Fiorillo et al., 2021).”
Jung, Y., Jeon, C., Kim, J., Jeong, H., Jun, S., & Ha, B. (2012) · doi:10.1039/c1sm05706e · Cited by 65 · cited 2×
“Snapshots of the fi nal con fi gurations at t = T f are shown above each plot, respectively. within con fi nements (Jun and Mulder, 2006; Jung and Ha, 2010; Jung et al., 2012; Junier et al., 2013; Wasim et al., 2021; Mitra et al., 2022a) have been previously been studied in computational settings.”
Bacterial chromatin: converging views at different scales.
Dame, R., & Tark-Dame, M. (2016) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2016.02.015 · Cited by 63 · cited 1× · see citing works
“Given the absence of NAPs structuring Syn3A ′ s chromosome into bacterial chromatin (Dame and Tark-Dame, 2016), we chose to model the chromosome of essentially naked dsDNA as a twistable and elastic worm-like chain (Klenin et al., 1998; Brackley et al., 2014; Maffeo and Aksimentiev, 2020).”
Orlandini, E., Marenduzzo, D., & Michieletto, D. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1815394116 · Cited by 63 · see citing works
Transient DNA Occupancy of the SMC Interarm Space in Prokaryotic Condensin
Nunez, R. J. V., Avila, L. B. R., & Gruber, S. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.05.001 · Cited by 61 · see citing works
Theoretical models for single-molecule DNA and RNA experiments: from elasticity to unzipping
Cocco, S., Marko, J. F., & Monasson, R. (2002) · doi:10.1016/s1631-0705(02)01345-2 · Cited by 60 · cited 1×
“…interact through stretching, bending, and twisting potentials (Figure 1C) that reproduce the tensile, bending, and torsional stiffness of dsDNA (Cocco et al., 2002; Brackley et al., 2014), and are parameterized by linear (45 nm) (Manning, 2006; Geggier et al., 2010; Mantelli et al., 2011) and…”
Junier, I., Boccard, F., & Espéli, O. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1005 · Cited by 59 · see citing works
Segregation of the Escherichia coli chromosome terminus
Li, Y., Youngren, B., Sergueev, K. V., & Austin, S. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03746.x · Cited by 58 · see citing works
Marko, J. (2009) · Physical review. E, Statistical, nonlinear, and soft matter physics · doi:10.1103/physreve.79.051905 · Cited by 57 · cited 5×
“Both chromosome disentanglement through the in fl uence of compaction (Goloborodko et al., 2016b) caused by DNA-looping (Marko, 2009; 2011; Goloborodko et al., 2016a; Brahmachari and Marko, 2019) and the partitioning of chromosomes through entropic repulsion of polymer topologies ccwi ) as a…”
InfluentialŚmigiel, W., Mantovanelli, L., Linnik, D. S., Punter, M., Silberberg, J., Xiang, L.-M., Xu, K., & Poolman, B. (2022) · Science Advances · doi:10.1126/sciadv.abo5387 · Cited by 54
Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures
Brahmachari, S., & Marko, J. F. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1906355116 · Cited by 54 · see citing works
Mechanisms for Chromosome Segregation in Bacteria
Gogou, C., Japaridze, A., & Dekker, C. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.685687 · Cited by 53 · cited 2× · see citing works
“…al., 2014; Khan et al., 2016; Wasim et al., 2021; Pountain et al., 2022) and for the segregation of daughter chromosomes (Goloborodko et al., 2016a; Gogou et al., 2021) under the in fl uence of known essential components (Breuer et al., 2019), SMC-complexes (Ganji et al., 2018; Lee et al., 2021)…”
Hallock, M. J., Stone, J. E., Roberts, E., Fry, C., & Luthey-Schulten, Z. (2014) · Parallel Computing · doi:10.1016/j.parco.2014.03.009 · Cited by 50 · see citing works
Self-citationThe 3D Genome Structure of Single Cells
Zhou, T., Zhang, R., & Ma, J. (2021) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-020121-084709 · Cited by 50 · see citing works
Detecting chromatin interactions between and along sister chromatids with SisterC
Oomen, M. E., Hedger, A. K., Watts, J. K., & Dekker, J. (2020) · Nature Methods · doi:10.1038/s41592-020-0930-9 · Cited by 49 · see citing works
Direct Evidence for the Formation of Precatenanes during DNA Replication
Cebrián, J., Castán, A., Martínez, V., Kadomatsu-Hermosa, M. J., Parra, C., Fernández-Nestosa, M. J., Schaerer, C. E., Hernández, P., Krimer, D. B., & Schvartzman, J. B. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.642272 · Cited by 48 · see citing works
Nomidis, S. K., Carlon, E., Gruber, S., & Marko, J. (2022) · bioRxiv · doi:10.1093/nar/gkac268 · Cited by 48 · see citing works
Multiscale Dynamic Structuring of Bacterial Chromosomes.
Lioy, V. S., Junier, I., & Boccard, F. (2021) · Annual Review of Microbiology · doi:10.1146/annurev-micro-033021-113232 · Cited by 48 · cited 2× · see citing works
“Beyond the information stored in the sequence of the genome, the 3D organization of eukaryotic (Kempfer and Pombo, 2019) and bacterial (Dame et al., 2019; Lioy et al., 2021) genomes plays a role in cellular behavior (Dekker and Mirny, 2016).”
Distinct activities of bacterial condensins for chromosome management in Pseudomonas aeruginosa
Lioy, V. S., Junier, I., Lagage, V., Vallet, I., & Boccard, F. (2020) · bioRxiv · doi:10.1101/2020.05.18.101659 · Cited by 48
Theory and simulations of condensin mediated loop extrusion in DNA
Takaki, R., Dey, A., Shi, G., & Thirumalai, D. (2021) · Nature Communications · doi:10.1038/s41467-021-26167-1 · Cited by 48 · cited 1× · see citing works
“Based on step-size distributions measured with magnetic tweezers (Ryu et al., 2021) and analytical calculations (Takaki et al., 2021), we chose these to be L ext-avg = 20 monomers (68 nm) and L ext-max = 30 monomers (102 nm).”
Shimizu, M., Noguchi, Y., Sakiyama, Y., Kawakami, H., Katayama, T., & Takada, S. (2016) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1609649113 · Cited by 46
Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS.
Brackley, C., Morozov, A., & Marenduzzo, D. (2014) · Journal of Chemical Physics · doi:10.1063/1.4870088 · Cited by 46 · see citing works
The macro and micro of chromosome conformation capture
Goel, V. Y., & Hansen, A. S. (2020) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.395 · Cited by 46 · cited 1× · see citing works
“Following the creation of 3C, many variations have been developed (Denker and de Laat, 2016; Goel and Hansen, 2020), the most well-known of which is perhaps Hi-C (Lieberman-Aiden et al., 2009).”
InfluentialIn Cell Protein-Protein Contacts: Transient Interactions in the Crowd.
Rickard, M., Zhang, Y., Gruebele, M., & Pogorelov, T. (2019) · Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.9b01556 · Cited by 45 · see citing works
Chromatin Loop Extrusion and Chromatin Unknotting
Račko, D., Benedetti, F., Goundaroulis, D., & Stasiak, A. (2018) · Polymers · doi:10.3390/polym10101126 · Cited by 43 · cited 1× · see citing works
“…forces and lowered barriers enable the departure from a local energy minimum with a more-knotted topology into a new energy minimum with a less-knotted topology, which is consistent with previous computational studies on knotted chromosome topologies (Racko et al., 2018; Orlandini et al., 2019).”
An elementary singularity-free Rotational Brownian Dynamics algorithm for anisotropic particles.
Ilie, I., Briels, W., & den Otter, W. D. (2015) · Journal of Chemical Physics · doi:10.1063/1.4914322 · Cited by 42 · cited 1×
“The time-integration was carried out using an OpenMP-accelerated version of the Brownian dynamics integrator for aspherical particles (Delong et al., 2015; Ilie et al., 2015) in LAMMPS (Thompson et al., 2022).”
Shapes of semiflexible polymers in confined spaces
Liu, Y., & Chakraborty, B. (2007) · Physical Biology · doi:10.1088/1478-3975/5/2/026004 · Cited by 42
Diversity and Functions of Type II Topoisomerases
Sutormin, D. A., Galivondzhyan, A., Polkhovskiy, A., Kamalyan, S., Severinov, K., & Dubiley, S. A. (2021) · Acta Naturae · doi:10.32607/actanaturae.11058 · Cited by 41 · see citing works
Marucci, L., Barberis, M., Karr, J. R., Ray, O., Race, P., Andrade, M. D. S., Grierson, C., Hoffmann, S. A., Landon, S., Rech, E., et al. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.00942 · Cited by 39 · see citing works
Iterative annealing mechanism explains the functions of the GroEL and RNA chaperones
Thirumalai, D., Lorimer, G., & Hyeon, C. (2019) · Protein Science · doi:10.1002/pro.3795 · Cited by 39 · see citing works
Direct observation of independently moving replisomes in Escherichia coli
Japaridze, A., Gogou, C., Kerssemakers, J., Nguyen, H. M., & Dekker, C. (2019) · Nature Communications · doi:10.1038/s41467-020-16946-7 · Cited by 37 · cited 1×
“Recent work has provided additional evidence for the train-track model by imaging independently moving replisomes using fl uorescently labeled β -clamps (DnaN) in E. coli cells with synchronized replication initiation (Japaridze et al., 2020).”
A Geometrical Model for DNA Organization in Bacteria
Buenemann, M., & Lenz, P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013806 · Cited by 34 · see citing works
Shi, G., & Thirumalai, D. (2023) · Nature Communications · doi:10.1038/s41467-023-36412-4 · Cited by 34 · see citing works
Messelink, J. J. B., van Teeseling, M. C. F., Janssen, J., Thanbichler, M., & Broedersz, C. (2021) · Nature Communications · doi:10.1038/s41467-021-22189-x · Cited by 33 · see citing works
Protein Assembly and Crowding Simulations
Heo, L., Sugita, Y., & Feig, M. (2022) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102340 · Cited by 32 · cited 1×
“Researchers have previously completed molecular dynamics (MD) simulations of representative volumes of bacterial cytoplasm (Yu et al., 2016; Rickard et al., 2019; Heo et al., 2022), but only recently has it become possible to prepare a MD simulation of an entire bacterium (Stevens et al., 2023).”
Gilbert, B. R., Thornburg, Z. R., Lam, V., Rashid, F.-Z. M., Glass, J. I., Villa, E., Dame, R. T., & Luthey-Schulten, Z. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.644133 · Cited by 30 · see citing works
Self-citationWasim, A., Gupta, A., & Mondal, J. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab094 · Cited by 30
Determining the Mesh Size of Polymer Solutions via the Pore Size Distribution
Sorichetti, V., Hugouvieux, V., & Kob, W. (2019) · Macromolecules · doi:10.1021/acs.macromol.9b02166 · Cited by 30 · cited 1×
“…(Figure 5C; Supplementary Material), we determined that this was a result of the system with bonds creating a polymer mesh with persistent voids (Sorichetti et al., 2020; Xiang et al., 2021) for the ribosomes to diffuse within, in contrast to the case without bonds where the DNA monomers…”
Mass spectrometry of hydrogen/deuterium exchange in 70S ribosomal proteins from E. coli
Yamamoto, T., Izumi, S., & Gekko, K. (2006) · FEBS Letters · doi:10.1016/j.febslet.2006.05.049 · Cited by 30 · cited 1×
“We model only complete 70S ribosomes with an assumed mass of 2,700 KDa (Yamamoto et al., 2006).”
Brownian motion of the wormlike chain and segmental diffusion of DNA
Berg, O. G. (1979) · doi:10.1002/bip.1979.360181114 · Cited by 30 · cited 2×
“…predictions ( α = 0.75) for short-time segmental motion in stiff worm-like chains with contour lengths much longer than their persistence length (Berg, 1979) and experimental measurements ( α = 0.75) of large (relative to void) particle diffusion in networks of stiff fi laments (Amblard et…”
InfluentialKhan, S. R., Mahaseth, T., Kouzminova, E. A., Cronan, G. E., & Kuzminov, A. (2016) · Genetics · doi:10.1534/genetics.115.184697 · Cited by 30 · see citing works
Sefer, E., Duggal, G., & Kingsford, C. (2015) · Annual International Conference on Research in Computational Molecular Biology · doi:10.1089/cmb.2015.0210 · Cited by 28 · see citing works
Genome-in-a-Box: Building a Chromosome from the Bottom Up
Birnie, A., & Dekker, C. (2020) · ACS Nano · doi:10.1021/acsnano.0c07397 · Cited by 28 · cited 1× · see citing works
“Syn3A is a compelling system for a systematic study of bacterial chromosomes (Birnie and Dekker, 2020), including but not limited to their replication and segregation, and the bacterial cell cycle (Olivi et al., 2021) because the protein functions encoded by its remaining essential genes…”
Shape transition of semi-flexible macromolecules confined in channel and cavity
Cifra, P., & Bleha, T. (2010) · The European Physical Journal E : Soft matter · doi:10.1140/epje/i2010-10626-y · Cited by 27
HBsu Is Required for the Initiation of DNA Replication in Bacillus subtilis
Karaboja, X., & Wang, X.-D. (2022) · Journal of Bacteriology · doi:10.1128/jb.00119-22 · Cited by 26 · cited 2×
“Additionally, HU is essential for replication initiation in Gram-positive B. subtilis (Karaboja and Wang, 2022; Schramm and Murray, 2022), whose replication origin is similarly a DnaA-based oriC .”
Extended sister-chromosome catenation leads to massive reorganization of the E. coli genome
Conin, B., Billault-Chaumartin, I., Sayyed, H. E., Quenech’du, N., Cockram, C. A., Koszul, R., & Espéli, O. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac105 · Cited by 26
Identification of a basal system for unwinding a bacterial chromosome origin
Richardson, T. T., Stevens, D., Pelliciari, S., Harran, O., Sperlea, T., & Murray, H. (2019) · EMBO Journal · doi:10.15252/embj.2019101649 · Cited by 25 · see citing works
Jung, Y., & Ha, B. (2010) · Physical review. E, Statistical, nonlinear, and soft matter physics · doi:10.1103/physreve.82.051926 · Cited by 25 · cited 2×
“Snapshots of the fi nal con fi gurations at t = T f are shown above each plot, respectively. within con fi nements (Jun and Mulder, 2006; Jung and Ha, 2010; Jung et al., 2012; Junier et al., 2013; Wasim et al., 2021; Mitra et al., 2022a) have been previously been studied in computational settings.”
Lattice Models of Bacterial Nucleoids
Goodsell, D. S., Autin, L., & Olson, A. J. (2018) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.7b11770 · Cited by 24 · cited 1× · see citing works
“…models that can simulate entire bacterial chromosomes (Buenemann and Lenz, 2010; Messelink et al., 2021; Wasim et al., 2021), relatively few are at spatial resolutions less than hundreds to thousands of base pairs (bp) per particle (Hacker et al., 2017; Goodsell et al., 2018; Gilbert et al., 2021).”
Metabolite Damage and Damage Control in a Minimal Genome
(2022) · doi:10.1128/mbio.01630-22 · Cited by 24 · cited 1× · see citing works
“…through experimental charactizations of its biochemical components — genome-wide gene-essentiality and proteomics (Breuer et al., 2019), metabolomics (Haas et al., 2022), lipidomics (Thornburg et al., 2022), and cellular architecture from cryo-electron tomography (cryo-ET) (Gilbert et al., 2021).”
Self-citationIntegrating cellular and molecular structures and dynamics into whole-cell models
Luthey-Schulten, Z., Thornburg, Z. R., & Gilbert, B. R. (2022) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102392 · Cited by 23 · see citing works
Self-citationHigh-Resolution Whole-Genome Analysis of Sister-Chromatid Contacts.
Espinosa, E., Paly, E., & Barre, F. (2020) · Molecules and Cells · doi:10.1016/j.molcel.2020.06.033 · Cited by 22
Sekelja, M., Paulsen, J., & Collas, P. (2016) · Genome Biology · doi:10.1186/s13059-016-0923-2 · Cited by 22 · see citing works
Kinetic modeling of the genetic information processes in a minimal cell
Thornburg, Z. R., Melo, M. C. R., Bianchi, D., Brier, T. A., Crotty, C., Breuer, M., Smith, H. O., Hutchison, C. A., Glass, J. I., & Luthey-Schulten, Z. (2019) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2019.00130 · Cited by 22 · cited 3× · see citing works
“…2000), we believe a small number of HU was retained to ful fi ll an essential role during replication initiation using a DnaA-based oriC in Syn3A (Thornburg et al., 2019), but do not expect it to in fl uence chromosome-scale organization with its reduced proteomics count, and therefore exclude HU…”
InfluentialSelf-citationThree-dimensional loop extrusion
Bonato, A., & Michieletto, D. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.11.015 · Cited by 22 · cited 3× · see citing works
“There are two possible events during these hinge-update steps (Bonato and Michieletto, 2021) — 1) intra-strand motion in which the hinge advances in 1D along the current strand in the previously assigned direction or 2) inter-strand motion in which the hinge unbinds from the current strand with…”
Modeling the 3D Conformation of Genomes
Tiana, G., & Luca, G. (2019) · doi:10.1201/9781315144009 · Cited by 21 · cited 1×
“…have a stunning breadth of experimental data characterizing interactions throughout the genome, computational models (Rosa and Zimmer, 2014; Tiana and Giorgetti, 2019) are required to solve the inverse problem of determining 3D genome organization (Di Pierro et al., 2017; Messelink et al.,…”
Marko, J. (2011) · Journal of statistical physics · doi:10.1007/s10955-011-0172-4 · Cited by 21 · cited 5× · see citing works
“Both chromosome disentanglement through the in fl uence of compaction (Goloborodko et al., 2016b) caused by DNA-looping (Marko, 2009; 2011; Goloborodko et al., 2016a; Brahmachari and Marko, 2019) and the partitioning of chromosomes through entropic repulsion of polymer topologies ccwi ) as a…”
InfluentialOn the demultiplexing of chromosome capture conformation data
Junier, I., Spill, Y. G., Martı́-Renom, M. A., Beato, M., & Dily, F. L. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.05.049 · Cited by 20 · cited 2× · see citing works
“…replication states, this motivates the development of a protocol to deconvolve experimental maps generated from populations of unsynchronized cells (Junier et al., 2015; Sefer et al., 2016; Carstens et al., 2020; Zhou et al., 2021; Rowland et al., 2022) to determine the subpopulations of cells in…”
Yoshida, R., Ozaki, S., Kawakami, H., & Katayama, T. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad389 · Cited by 19
Bayesian inference of chromatin structure ensembles from population-averaged contact data
Carstens, S., Nilges, M., & Habeck, M. (2020) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1910364117 · Cited by 19 · see citing works
A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation
Geng, Y., Bohrer, C., Yehya, N. N., Hendrix, H., Shachaf, L., Liu, J., Xiao, J., & Roberts, E. (2022) · PLoS Comput. Biol. · doi:10.1371/journal.pcbi.1009788 · Cited by 18 · see citing works
Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data
Kos, P., Galitsyna, A., Ulianov, S., Gelfand, M., Razin, S., & Chertovich, A. (2021) · PLoS Comput. Biol. · doi:10.1371/journal.pcbi.1009546 · Cited by 17 · see citing works
DNA Supercoiling Drives a Transition between Collective Modes of Gene Synthesis
Chatterjee, P., Goldenfeld, N., & Kim, S. (2021) · bioRxiv · doi:10.1103/physrevlett.127.218101 · Cited by 17 · cited 2× · see citing works
“…(Lioy et al., 2018) when its expression is restored and to mechanochemically couple transcriptional activity in the 4D-WCM to the torsional state of the chromosome (Liu and Wang, 1987; Chong et al., 2014; Dorman, 2019; Kim et al., 2019; Chatterjee et al., 2021; Guo et al., 2021; Geng et al., 2022).”
Verma, S. C., Harned, A., Narayan, K., & Adhya, S. (2023) · Molecular Microbiology · doi:10.1111/mmi.15033 · Cited by 16 · see citing works
Metabolomic analysis of sulfur-containing substances and polyamines in regenerating rat liver
Jung, Y. S., Kim, S., Kwon, D., & Kim, Y. (2012) · Amino Acids · doi:10.1007/s00726-011-0946-7 · Cited by 16
Structure-function relationships of SMC protein complexes for DNA loop extrusion
Lee, H., Noh, H., & Ryu, J. (2021) · Korean Society for Structural Biology · doi:10.34184/kssb.2021.9.1.1 · Cited by 15 · cited 3× · see citing works
“After accounting for the 4:2:4 stoichiometry (Lee et al., 2021) of E. coli ′ s SMC complex, MukBEF, we fi nd that the densities of SMC core proteins per bp of genome are ranked in decreasing order as 1) E. coli , 2) Syn3A, 3) B. subtilis (Table 1).”
Beyond histograms: Efficiently estimating radial distribution functions via spectral Monte Carlo
Patrone, P. N., & Rosch, T. W. (2017) · The Journal of Chemical Physics · doi:10.1063/1.4977516 · Cited by 13 · see citing works
Strzałka, A., Kois-Ostrowska, A., Kędra, M., Łebkowski, T., Bieniarz, G., Szafran, M., & Jakimowicz, D. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1093 · Cited by 13
Speed variations of bacterial replisomes
Bhat, D., Hauf, S., Plessy, C., Yokobayashi, Y., & Pigolotti, S. (2022) · eLife · doi:10.7554/elife.75884 · Cited by 13 · cited 1× · see citing works
“…of sequence-equivalent contact maps for replication microstates and 2) even with that information, the problem likely remains underdetermined if only subject to the example set of constraints (Section 2.5) and not more informative constraints such as DNA abundance distributions (Bhat et al., 2022).”
InfluentialRideau, F., Villa, A., Belzanne, P., Verdier, E., Hosy, E., & Arfi, Y. (2022) · bioRxiv · doi:10.1128/spectrum.00645-22 · Cited by 12 · see citing works
THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data
Rowland, B., Huh, R., Hou, Z., Crowley, C., Wen, J., Shen, Y., Hu, M., Giusti‐Rodríguez, P., Sullivan, P. F., & Li, Y. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010102 · Cited by 11 · see citing works
Mitra, D., Pande, S., & Chatterji, A. (2022) · Soft Matter · doi:10.1039/d2sm00734g · Cited by 11 · cited 1× · see citing works
“Previous simulations of replicating chromosomes have used either a set of fi xed replication states (Wasim et al., 2021; 2023; Mitra et al., 2022b) or a pre-de fi ned replication protocol (Mitra et al., 2022a).”
Interpretation of Organizational Role of Proteins on E. coli Nucleoid via Hi-C integrated Model.
Wasim, A., Gupta, A., Bera, P., & Mondal, J. (2022) · Biophysical Journal · doi:10.1016/j.bpj.2022.11.2938 · Cited by 10
Hybrid CME–ODE method for efficient simulation of the galactose switch in yeast
Bianchi, D. M., Peterson, J. R., Earnest, E. E., Hallock, M. J., & Luthey‐Schulten, Z. (2018) · IET Systems Biology · doi:10.1049/iet-syb.2017.0070 · Cited by 8 · see citing works
Self-citationTopology-driven spatial organization of ring polymers under confinement.
Mitra, D., Pande, S., & Chatterji, A. (2022) · Physical Review E · doi:10.1103/physreve.106.054502 · Cited by 7
Dersch, S., Rotter, D. A., & Graumann, P. (2022) · Microbial Physiology · doi:10.1159/000526846 · Cited by 6 · cited 1×
“…than other bacteria (Gilbert et al., 2021) and the chromosome itself, through excluded volume interactions with other macromolecular complexes (Dersch et al., 2022) and spatially localized transcription (Llopis et al., 2010), potentially represents the greatest in fl uence on spatially…”
Transcription-replication interactions reveal principles of bacterial genome regulation
Pountain, A. W., Jiang, P., Yao, T.-Y., Homaee, E., Guan, Y., Podkowik, M., Shopsin, B., Torres, V., Golding, I., & Yanai, I. (2023) · bioRxiv · doi:10.21203/rs.3.rs-2724389/v1 · Cited by 5
HU content and dynamics in Escherichia coli during the cell cycle and at different growth rates
Abebe, A. H., Aranovich, A., & Fishov, I. (2017) · FEMS Microbiology Letters · doi:10.1093/femsle/fnx195 · Cited by 5 · see citing works
6 – Langevin and Generalised Langevin Dynamics
Snook, I. (2006) · doi:10.1016/b978-044452129-3/50007-9 · Cited by 5 · cited 3×
“The Brownian equation of motion d x i d t approximates the overdamped limit of the Langevin equation and is only an accurate approximation if the inertial forces are insigni fi cant compared to the viscous forces (Snook, 2007).”
Single-molecule biophysics experiments in silico: Toward a physical model of a replisome
Maffeo, C. M., Chou, H.-Y. E., & Aksimentiev, A. (2021) · bioRxiv · doi:10.1016/j.isci.2022.104264 · Cited by 4 · see citing works
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Cited by
Sorted by citations
Bringing the genetically minimal cell to life on a computer in 4D
Thornburg, Z. R., Maytin, A., Kwon, J., Brier, T. A., Gilbert, B. R., Fu, E., Gao, Y.-L., Quenneville, J., Wu, T., Li, H., et al. (2026) · Cell · doi:10.1016/j.cell.2026.02.009 · Cited by 44 · see citing works
Self-citationDe novo design of synthetic microbial genomes
Koster, C. C., Oliveira, H. D. C., van Beveren, F., Houkes, J., van Hooff, J. J. E., Ettema, T. J. G., John van der, O. O. S. T., & Claassens, N. J. (2026) · Nature Reviews Bioengineering · doi:10.1038/s44222-026-00410-0 · Cited by 8 · see citing works
Compartment‐guided assembly of large‐scale molecular models with Bentopy
Westendorp, M. S. S., Stevens, J., Brown, C., Dommer, A., Wassenaar, T., Bruininks, B., & Marrink, S. (2026) · Protein Science · doi:10.1002/pro.70480 · Cited by 7 · see citing works
Self-citationIntegrative modeling of JCVI-Syn3A nucleoids with a modular approach
Goodsell, D. S., & Autin, L. (2024) · Current Research in Structural Biology · doi:10.1016/j.crstbi.2023.100121 · Cited by 6 · see citing works
Coarse-Grained Simulations Reveal Salt- and Length-Dependent Condensation of G4C2 RNA Repeats.
Zhang, Q., Valério, M., Grünewald, L., Borges-Araújo, L., Grünewald, F., Wang, S.-M., Marrink, S., Gong, Y.-B., & Souza, P. C. T. (2026) · Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.6c00916 · Cited by 5 · see citing works
Self-citationAll-atom virus simulations to tackle airborne disease.
Dommer, A., Wauer, N. A., Marrink, S., & Amaro, R. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103048 · Cited by 5 · see citing works
Self-citationExploring the energy landscape of bacterial chromosome segregation
Brahmachari, S., Oliveira, A. B., Mello, M. F., Contessoto, V. G., & Onuchic, J. (2026) · bioRxiv · doi:10.1101/2024.07.27.604869 · Cited by 3
“Explicit dynamic modeling of strand passage by topoisomerase enzymes has observed their importance in preventing catastrophic DNA entanglements during both bacterial [25, 26] and eukaryotic replication [37].”
Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell
Fu, E., Thornburg, Z. R., Brier, T. A., Wei, R., Yuan, B., Gilbert, B. R., Wang, S., & Luthey-Schulten, Z. A. (2025) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c04532 · Cited by 2 · see citing works
Self-citationThe role of macromolecular crowders in the formation and compaction of the Escherichia coli nucleoid
Männik, J., Männik, J., Amarasinghe, C., Chang, M.-H., & Lavrentovich, M. O. (2025) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0002-2024 · Cited by 3 · see citing works
Maria, M., Guillaume, V., Guionnière, S., Dacquay, N., Plateau-Holleville, C., Larroque, V., Larde, J., Naimi, Y., Piquemal, J.-P., Levieux, G., et al. (2025) · Frontiers Bioinform. · doi:10.3389/fbinf.2025.1588661 · Cited by 2 · see citing works
“Additionally, modern high-performance computing hardware has enabled the simulation of larger molecular systems [6, 7, 8, 9], further amplifying data production.”
Johnson, C. G. M., Chan, A. N., Rozum, J. C., George, A., Parvate, A. D., Kim, D. N., Feng, S., Bohutskyi, P., Johnson, Z., Sadler, N. C., et al. (2026) · bioRxiv · doi:10.64898/2026.01.21.700212 · Cited by 1
“We used the packed genome configuration as an input to Brownian dynamics (BD) simulation, which simulates chromosome dynamics, using btree_chromo (55) and LAMMPS (56) in order to initialize gene placement within the cell.”
Self-citationRoure, G., Sivasankar, V. S., & Zia, R. N. (2025) · doi:10.1101/2025.08.16.670686 · Cited by 1 · see citing works
Memory effects of transcription regulator−DNA interactions in bacteria
Jung, W., Chen, T.-Y., Santiago, A. G., & Chen, P. (2024) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.2407647121 · Cited by 1
“However, recent research has produced increasingly compelling evidence that bacterial cells exhibit a remarkable level of spatial organizations in their cellular components independent of membranes ( 45 – 48 ).”
Chromosome segregation in a minimal bacterial cell driven by SMC protein complexes
Maytin, A. K., Gilbert, B. R., & Luthey-Schulten, Z. (2026) · Protein Science · doi:10.1002/pro.70604
“Previously, we developed a binary tree formalism to describe the replication state of the circular JCVI-Syn3A chromosome and used it to generate in silico contact maps for chromosomes in a wide range of replication configurations, including nested theta structures (Gilbert et al., 2023).”
InfluentialSelf-citationCondensate-Like Organization in Respiratory Aerosols Modulates the Dynamics of an Airborne VirusPreprint
Wauer, N. A., Calvó-Tusell, C., Dommer, A., Casalino, L., Kearns, F. L., Caparotta, M., Rosenfeld, M. A., Morris, C. K., & Amaro, R. (2026) · bioRxiv · doi:10.64898/2026.04.30.721971
“Similar behavior has been observed in large-scale simulations of influenza virions 24 , where hemagglutinin exhibited head “breathing” motion on a densely packed virion surface, with these motions accompanied by enhanced interplay with neighboring glycoproteins.”
Gene loci fluctuations reveal bacterial chromosome dynamical organization
Bajpai, G., Safran, S., Stavans, J., & Arbel-Goren, R. (2025) · Communications Biology · doi:10.1038/s42003-025-09200-7
“The contribution of these factors to genome compaction is still under debate and the focus of intense, current study 1,18,20 – 22 .”
Tuning a predictive DNA replication programming computational model for Trypanosomatids
Scholl, B. B., Palma, L., Hariki, V. S., Elias, M. C., & Reis, M. S. (2024) · Brazilian Symposium on Bioinformatics · doi:10.5753/bsb.2024.245608
“In 2023, Gilbert et al. proposed a model of the 3D dynamics of the chromosome in genetically minimal bacteria, called JCVI-syn3A, at a high spatial resolution of 10 base pairs (bp) per particle (Gilbert et al. 2023).”
- Authors
- Gilbert, B. R., Thornburg, Z. R., Brier, T. A., Stevens, J. A., Grünewald, F., Stone, J. E., Marrink, S. J., & Luthey-Schulten, Z.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- University of Groningen (NL)
- Corresponding author
- Luthey-Schulten, Zaida
- ORCID
- Venue
- Frontiers in Cell and Developmental Biology
- Publisher
- Frontiers Media SA
- Published
- 2023-08-09
- Volume
- 11
- Pages
- 1214962-1214962
- ISSN
- 2296-634X (ISSN-L)
- PMC
- PMC10445541
- OpenAlex
- W4385708092
- Cited by
- 19
- References
- 208
- Citations by year
- 2026: 9 · 2025: 6 · 2024: 3 · 2023: 1
- FWCI
- 1.69
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Cell and Developmental Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
- Funders
- National Science Foundation (2221237, 2014027, 1818344)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWA.1292.19.170)
- National Institutes of Health (GM104601, NIH P41-GM104601)
- University of Illinois at Urbana-Champaign
- National Institute of General Medical Sciences (P41GM104601, R24GM145965)
- Division of Molecular and Cellular Biosciences (MCB-1818344)
- HORIZON EUROPE European Research Council (101053661)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- bacterial chromosome organization, Brownian dynamics, loop extrusion, structural maintenance of chromosomes, topoisomerases, chromosome segregation, theta replication, whole-cell model, Martini coarse-grained model
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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