Probability of graphs with large spectral gap by multicanonical Monte Carlo

Graphs with large spectral gap are important in various fields such as biology, sociology and computer science. In designing such graphs, an important question is how the probability of graphs with large spectral gap behaves. A method based on multicanonical Monte Carlo is introduced to quantify the behavior of this probability, which enables us to calculate extreme tails of the distribution. The proposed method is successfully applied to random 3-regular graphs and large deviation probability is estimated.Comment: 3pages 4figure

Sampling motif-constrained ensembles of networks

The statistical significance of network properties is conditioned on null models which satisfy spec- ified properties but that are otherwise random. Exponential random graph models are a principled theoretical framework to generate such constrained ensembles, but which often fail in practice, either due to model inconsistency, or due to the impossibility to sample networks from them. These problems affect the important case of networks with prescribed clustering coefficient or number of small connected subgraphs (motifs). In this paper we use the Wang-Landau method to obtain a multicanonical sampling that overcomes both these problems. We sample, in polynomial time, net- works with arbitrary degree sequences from ensembles with imposed motifs counts. Applying this method to social networks, we investigate the relation between transitivity and homophily, and we quantify the correlation between different types of motifs, finding that single motifs can explain up to 60% of the variation of motif profiles.Comment: Updated version, as published in the journal. 7 pages, 5 figures, one Supplemental Materia

Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution

The aim of this paper is two-fold. First, we propose a new computational method to investigate the particularities of evolution. Second, we apply this method to a model of gene regulatory networks (GRNs) and explore the evolution of mutational robustness and bistability. Living systems have developed their functions through evolutionary processes. To understand the particularities of this process theoretically, evolutionary simulation (ES) alone is insufficient because the outcomes of ES depend on evolutionary pathways. We need a reference system for comparison. An appropriate reference system for this purpose is an ensemble of the randomly sampled genotypes. However, generating high-fitness genotypes by simple random sampling is difficult because such genotypes are rare. In this study, we used the multicanonical Monte Carlo method developed in statistical physics to construct a reference ensemble of GRNs and compared it with the outcomes of ES. We obtained the following results. First, mutational robustness was significantly higher in ES than in the reference ensemble at the same fitness level. Second, the emergence of a new phenotype, bistability, was delayed in evolution. Third, the bistable group of GRNs contains many mutationally fragile GRNs compared with those in the non-bistable group. This suggests that the delayed emergence of bistability is a consequence of the mutation-selection mechanism.Kaneko T., Kikuchi M.. (2022) Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution. PLoS Computational Biology 18(1): e1009796. doi: 10.1371/journal.pcbi.1009796

Emergence of cooperative bistability and robustness of gene regulatory networks

Gene regulatory networks (GRNs) are complex systems in which many genes regulate mutually to adapt the cell state to environmental conditions. In addition to function, the GRNs possess several kinds of robustness. This robustness means that systems do not lose their functionality when exposed to disturbances such as mutations or noise, and is widely observed at many levels in living systems. Both function and robustness have been acquired through evolution. In this respect, GRNs utilized in living systems are rare among all possible GRNs. In this study, we explored the fitness landscape of GRNs and investigated how robustness emerged in highly-fit GRNs. We considered a toy model of GRNs with one input gene and one output gene. The difference in the expression level of the output gene between two input states, “on” and “off”, was considered as fitness. Thus, the determination of the fitness of a GRN was based on how sensitively it responded to the input. We employed the multicanonical Monte Carlo method, which can sample GRNs randomly in a wide range of fitness levels, and classified the GRNs according to their fitness. As a result, the following properties were found: (1) Highly-fit GRNs exhibited bistability for intermediate input between “on” and “off”. This means that such GRNs responded to two input states by using different fixed points of dynamics. This bistability emerges necessarily as fitness increases. (2) These highly-fit GRNs were robust against noise because of their bistability. In other words, noise robustness is a byproduct of high fitness. (3) GRNs that were robust against mutations were not extremely rare among the highly-fit GRNs. This implies that mutational robustness is readily acquired through the evolutionary process. These properties are universal irrespective of the evolutionary pathway, because the results do not rely on evolutionary simulation.Nagata S., Kikuchi M..(2020) Emergence of cooperative bistability and robustness of gene regulatory networks. PLoS Computational Biology 16(6): 1007969. doi: 10.1371/journal.pcbi.1007969

Report / Institute für Physik

The 2014 Report of the Physics Institutes of the Universität Leipzig presents a hopefully interesting overview of our research activities in the past year. It is also testimony of our scientific interaction with colleagues and partners worldwide. We are grateful to our guests for enriching our academic year with their contributions in the colloquium and within the work groups. The open full professorship in the Institute for Experimental Physics I has been filled with an outstanding candidate. We could attract Prof. Ralf Seidel from the University of Münster. He is an expert in molecular biophysics that complements the existing strength in cellular biophysics. Prof. Hollands could fill all positions of his ERC Starting Grant, so that the work on the project \"Quantum Fields and Curvature – Novel Constructive Approach via Operator Product Expansion\" is now running at full pace. Within the Horizon 2020 project LOMID \"Large Cost-effective OLED Microdisplays and their Applications\" (2015-2017) with eight European partners including industry the semiconductor physics group contributes with transparent oxide devices. A joint laboratory for single ion implantation was established between the Leibniz-Institute for Surface Modification (IOM) and the university under the guidance of Profs. Rauschenbach and Meijer. The EU IRSES Network DIONICOS \"Dynamics of and in Complex Systems\", a consortium of 6 European and 12 non-European partners, including sites in England, France and Germany as well as in Russia, Ukraine, India, the United States and Venezuela, started in February 2014. In the next four years the Leipzig node headed by Prof. Janke will profit from the numerous international contacts this network provides. With a joint project, Prof. Kroy and Prof. Cichos participate in the newly established priority research programme SPP 1726 \"Microswimmers\", which started with a kick-off workshop in October 2014. In 2014 the International Graduate College \"Statistical Physics of Complex Systems\" run by the computational physics group has commenced its third 3-years granting period funded by Deutsch-Französische Hochschule (DFH-UFA). Besides the main partner Université de Lorraine in Nancy, France, now also Coventry University, UK, and the Institute for Condensed Matter Physis of the National Academy of Sciences of Ukraine in Lviv, Ukraine, participate as associated partners. During the last week of September the TCO2014 conference \"Transparent Conductive Oxides – Fundamentals and Applications\" took place in honor of the 100th anniversary of the death of Prof. Dr. KarlW. Bädeker. In 1907 Karl Bädeker had discovered transparent conductive materials and oxides in Leipzig. About a hundred participants joined for many invited talks from international experts, intense discussion and new cooperations. At the end of November the by now traditional 15th nternational Workshop on Recent Developments in Computational Physics \"CompPhys14\" organized by Prof. Janke took place in Leipzig. Around 60 scientists from over 10 different countries exchanged ideas and discussed recent progress in several fields of computational physics. Work has successfully continued in the Centers of Excellence (Sonderforschungsbereiche) SFB 762 \"Functionality ofOxide Interfaces\" and SFB TRR 102 \"Polymers under Multiple Constraints: Restricted and Controlled Molecular Order and Mobility\" (just renewed for 2015-2019). Our activities and success are only possible with the generous support fromvarious funding agencies for which we are very grateful and which is individually acknowledged in the brief reports

Report / Institute für Physik

The 2016 Report of the Physics Institutes of the Universität Leipzig presents a hopefully interesting overview of our research activities in the past year. It is also testimony of our scientific interaction with colleagues and partners worldwide. We are grateful to our guests for enriching our academic year with their contributions in the colloquium and within our work groups