arXiv subjects

Sander J. Tans

Publications and source records attributed to Sander J. Tans.

4 recordsLinked to original sources

arXiv2022

Defect dynamics in growing bacterial colonies

Colonies of rod-shaped bacteria constitute a system of colloidal active matter with nematic properties. As a single initial bacterium multiplies through repeated divisions, the resulting colony quickly loses long-range orientational order, but retains locally ordered domains. At the boundaries of these domains, topological defects emerge, which move around randomly as the colony grows. In both experiments and simulations, we find that these defects are created at a rate that corresponds to the exponential growth of the colony, resulting in a stable defect density. Both this defect density and the colony's correlation length are regulated by the aspect ratio of the rod-shaped particles. Moreover, we find that the defect dynamics are well described by a Gamma distribution, which is due to repeated divisions and subsequent re-orientations of the bacteria.

physics.bio-ph↗

arXiv2018

A graph-based algorithm for the multi-objective optimization of gene regulatory networks

The evolution of gene regulatory networks in variable environments poses Multi-objective Optimization Problem (MOP), where the expression levels of genes must be tuned to meet the demands of each environment. When formalized in the context of monotone systems, this problem falls into a sub-class of linear MOPs. Here, the constraints are partial orders and the objectives consist of either the minimization or maximization of single variables, but their number can be very large. To efficiently and exhaustively find Pareto optimal solutions, we introduce a mapping between coloured Hasse diagrams and polytopes associated with an ideal point. A dynamic program based on edge contractions yields an exact closed-form description of the Pareto optimal set, in polynomial time of the number of objectives relative to the number of faces of the Pareto front. We additionnally discuss the special case of series-parallel graphs with monochromatic connected components of bounded size, for which the running time and the representation of solutions can in principle be linear in the number of objectives.

math.OC↗

arXiv2017

Information-theoretic analysis of the directional influence between cellular processes

Inferring the directionality of interactions between cellular processes is a major challenge in systems biology. Time-lagged correlations allow to discriminate between alternative models, but they still rely on assumed underlying interactions. Here, we use the transfer entropy (TE), an information-theoretic quantity that quantifies the directional influence between fluctuating variables in a model-free way. We present a theoretical approach to compute the transfer entropy, even when the noise has an extrinsic component or in the presence of feedback. We re-analyze the experimental data from Kiviet et al. (2014) where fluctuations in gene expression of metabolic enzymes and growth rate have been measured in single cells of E. coli. We confirm the formerly detected modes between growth and gene expression, while prescribing more stringent conditions on the structure of noise sources. We furthermore point out practical requirements in terms of length of time series and sampling time which must be satisfied in order to infer optimally transfer entropy from times series of fluctuations.

q-bio.QM↗

arXiv1998

Imaging Electron Wave Functions of Quantized Energy Levels in Carbon Nanotubes

Carbon nanotubes provide a unique system to study one-dimensional quantization phenomena. Scanning tunneling microscopy is used to observe the electronic wave functions that correspond to quantized energy levels in short metallic carbon nanotubes. Discrete electron waves are apparent from periodic oscillations in the differential conductance as a function of the position along the tube axis, with a period that differs from that of the atomic lattice. Wave functions can be observed for several electron states at adjacent discrete energies. The measured wavelengths are in good agreement with the calculated Fermi wavelength for armchair nanotubes.

cond-mat.mes-hall↗