Alexander E. Lobkovsky

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The re-emergence of groundwater at the surface shapes the Earth’s topography through a process known as seepage erosion1–5. In combination with flow over land6, seepage erosion contributes to the initiation and growth of channel networks1–5. Seepage processes have also been invoked in the formation of enigmatic amphitheatre-headed channel networks on both(More)
A stochastic, agent-based mathematical model of the coevolution of the archaeal and bacterial adaptive immunity system, CRISPR-Cas, and lytic viruses shows that CRISPR-Cas immunity can stabilize the virus-host coexistence rather than leading to the extinction of the virus. In the model, CRISPR-Cas immunity does not specifically promote viral diversity,(More)
UNLABELLED Bacteria and archaea face continual onslaughts of rapidly diversifying viruses and plasmids. Many prokaryotes maintain adaptive immune systems known as clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (Cas). CRISPR-Cas systems are genomic sensors that serially acquire viral and plasmid DNA fragments(More)
Motivated by examples of erosive incision of channels in sand, we investigate the motion of individual grains in a granular bed driven by a laminar fluid to give us new insights into the relationship between hydrodynamic stress and surface granular flow. A closed cell of rectangular cross-section is partially filled with glass beads and a constant fluid(More)
[1] We propose a dynamical model for channels incised into an erodible bed by subsurface water flow. The model is validated by the time-resolved topographic measurements of channel growth in a laboratory-scale experiment. Surface heights in the experiment are measured via a novel laser-aided imaging technique. The erosion rate in the model is composed of(More)
Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness landscape. We report an exhaustive analysis of fitness landscapes constructed with an off-lattice model of protein folding(More)
The hypothesis that folding robustness is the primary determinant of the evolution rate of proteins is explored using a coarse-grained off-lattice model. The simplicity of the model allows rapid computation of the folding probability of a sequence to any folded conformation. For each robust folder, the network of sequences that share its native structure is(More)
Evolution of prokaryotes involves extensive loss and gain of genes, which lead to substantial differences in the gene repertoires even among closely related organisms. Through a wide range of phylogenetic depths, gene frequency distributions in prokaryotic pangenomes bear a characteristic, asymmetrical U-shape, with a core of (nearly) universal genes, a(More)
We compare the sets of experimentally validated long intergenic non-coding (linc)RNAs from human and mouse and apply a maximum likelihood approach to estimate the total number of lincRNA genes as well as the size of the conserved part of the lincRNome. Under the assumption that the sets of experimentally validated lincRNAs are random samples of the(More)
We analyze a two-dimensional phase field model designed to describe the dynamics of crystalline grains. The phenomenological free energy is a functional of two order parameters. The first one reflects the orientational order, while the second reflects the predominantally local orientation of the crystal. We consider the gradient flow of this free energy.(More)