arXiv subjects

Mislav Cvitković

Publications and source records attributed to Mislav Cvitković.

4 recordsLinked to original sources

arXiv2021

Crowding competes with trapping to enhance interfacial diffusion

Diffusion in the crowded environments of the biological membranes or materials interfaces often involves intermittent binding to surface proteins or defects. To account for this situation we study a 2-dimensional lattice gas in a field of immobilized traps. Using kinetic Monte Carlo simulations, we calculate the effective diffusion coefficient in the long-time limit as a function of the traps and particle densities. We find a remarkable result - an increase of the diffusion coefficient with particle density, an effect that we coin as crowding-enhanced diffusion. We rationalize this result using scaling arguments and the master equation approach.

cond-mat.soft↗

arXiv2018

Structural basis for the shielding function of the dynamic trypanosome variant surface glycoprotein coat

The most prominent defence of the unicellular parasite Trypanosoma brucei against the host immune system is a dense coat that comprises a variant surface glycoprotein (VSG). Despite the importance of the VSG family, no complete structure of a VSG has been reported. Making use of high-resolution structures of individual VSG domains, we employed small-angle X-ray scattering to elucidate the first two complete VSG structures. The resulting models imply that the linker regions confer great flexibility between domains, which suggests that VSGs can adopt two main conformations to respond to obstacles and changes of protein density, while maintaining a protective barrier at all times. Single-molecule diffusion measurements of VSG in supported lipid bilayers substantiate this possibility, as two freely diffusing populations could be detected. This translates into a highly flexible overall topology of the surface VSG coat, which displays both lateral movement in the plane of the membrane and variation in the overall thickness of the coat.

physics.bio-ph↗

arXiv2017

Asymptotic expansions of the hypergeometric function with two large parameters $-$ application to the partition function of a lattice gas in a field of traps

The canonical partition function of a two-dimensional lattice gas in a field of randomly placed traps, like many other problems in physics, evaluates to the Gauss hypergeometric function ${}_2F_1(a,b;c;z)$ in the limit when one or more of its parameters become large. This limit is difficult to compute from first principles, and finding the asymptotic expansions of the hypergeometric function is therefore an important task. While some possible cases of the asymptotic expansions of ${}_2F_1(a,b;c;z)$ have been provided in the literature, they are all limited by a narrow domain of validity, either in the complex plane of the variable or in the parameter space. Overcoming this restriction, we provide new asymptotic expansions for the hypergeometric function with two large parameters, which are valid for the entire complex plane of $z$ except for a few specific points. We show that these expansions work well even when we approach the possible singularity of ${}_2F_1(a,b;c;z)$, $|z|=1$, where the current expansions typically fail. Using our results we determine asymptotically the partition function of a lattice gas in a field of traps in the different possible physical limits of few/many particles and few/many traps, illustrating the applicability of the derived asymptotic expansions of the HGF in physics.

math-ph↗

arXiv2011

Large Tandem, Higher Order Repeats and Regularly Dispersed Repeat Units Contribute Substantially to Divergence Between Human and Chimpanzee Y Chromosomes

Comparison of human and chimpanzee genomes has received much attention, because of paramount role for understanding evolutionary step distinguishing us from our closest living relative. In order to contribute to insight into Y chromosome evolutionary history, we study and compare tandems, higher order repeats (HORs), and regularly dispersed repeats in human and chimpanzee Y chromosome contigs, using robust Global Repeat Map algorithm. We find a new type of long-range acceleration, human-accelerated HOR regions. In peripheral domains of 35mer human alphoid HORs, we find riddled features with ten additional repeat monomers. In chimpanzee, we identify 30mer alphoid HOR. We construct alphoid HOR schemes showing significant human-chimpanzee difference, revealing rapid evolution after human-chimpanzee separation. We identify and analyze over 20 large repeat units, most of them reported here for the first time as: chimpanzee and human ~1.6 kb 3mer secondary repeat unit (SRU) and ~23.5 kb tertiary repeat unit (~0.55 kb primary repeat unit, PRU); human 10848, 15775, 20309, 60910, and 72140 bp PRUs; human 3mer SRU (~2.4 kb PRU); 715mer and 1123mer SRUs (5mer PRU); chimpanzee 5096, 10762, 10853, 60523 bp PRUs; and chimpanzee 64624 bp SRU (10853 bp PRU). We show that substantial human-chimpanzee differences are concentrated in large repeat structures, at the level of as much as ~70% divergence, sizably exceeding previous numerical estimates for some selected noncoding sequences. Smeared over the whole sequenced assembly (25 Mb) this gives ~14% human--chimpanzee divergence. This is significantly higher estimate of divergence between human and chimpanzee than previous estimates.

q-bio.GN↗