Kinetics of self-assembly via facilitated diffusion: formation of the transcription complex

We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in three-dimensions and one-dimension. Our study is motivated by single molecule level observations revealing the dynamics of transcription factors that bind to the DNA at early stages of transcription. We calculate the probability that a complex made up of a given number of molecules is completely formed, as well as the distribution of completion times, upon the binding of a seed molecule at a target site on the filament (without explicitly modeling the three-dimensional diffusion that precedes binding). We compare two different mechanisms of assembly where molecules bind in sequential and random order. Our results indicate that while the probability of completion is greater for random binding, the completion time scales exponentially with the size of the complex; in contrast, it scales as a power-law or slower for sequential binding, asymptotically. Furthermore, we provide model predictions for the dissociation and residence times of the seed molecule, which are observables accessible in single molecule tracking experiments.Comment: to appear in Phys. Rev.

Fragmentation of Random Trees

We study fragmentation of a random recursive tree into a forest by repeated removal of nodes. The initial tree consists of N nodes and it is generated by sequential addition of nodes with each new node attaching to a randomly-selected existing node. As nodes are removed from the tree, one at a time, the tree dissolves into an ensemble of separate trees, namely, a forest. We study statistical properties of trees and nodes in this heterogeneous forest, and find that the fraction of remaining nodes m characterizes the system in the limit N --> infty. We obtain analytically the size density phi_s of trees of size s. The size density has power-law tail phi_s ~ s^(-alpha) with exponent alpha=1+1/m. Therefore, the tail becomes steeper as further nodes are removed, and the fragmentation process is unusual in that exponent alpha increases continuously with time. We also extend our analysis to the case where nodes are added as well as removed, and obtain the asymptotic size density for growing trees.Comment: 9 pages, 5 figure

Extensions of Effective Medium Theory of Transport in Disordered Systems

Effective medium theory of transport in disordered systems, whose basis is the replacement of spatial disorder by temporal memory, is extended in several practical directions. Restricting attention to a 1-dimensional system with bond disorder for specificity, a transformation procedure is developed to deduce, from given distribution functions characterizing the system disorder, explicit expressions for the memory functions. It is shown how to use the memory functions in the Lapace domain forms in which they first appear, and in the time domain forms which are obtained via numerical inversion algorithms, to address time evolution of the system beyond the asymptotic domain of large times normally treated. An analytic but approximate procedure is provided to obtain the memories, in addition to the inversion algorithm. Good agreement of effective medium theory predictions with numerically computed exact results is found for all time ranges for the distributions used except near the percolation limit as expected. The use of ensemble averages is studied for normal as well as correlation observables. The effect of size on effective mediumtheory is explored and it is shown that, even in the asymptotic limit, finite size corrections develop to the well known harmonic mean prescription for finding the effective rate. A percolation threshold is shown to arise even in 1-d for finite (but not infinite) systems at a concentration of broken bonds related to the system size. Spatially long range transfer rates are shown to emerge naturally as a consequence of the replacement of spatial disorder by temporal memories, in spite of the fact that the original rates possess nearest neighbor character. Pausing time distributions in continuous time random walks corresponding to the effective medium memories are calculated.Comment: 15 pages, 11 figure

Lagrange formulation of the symmetric teleparallel gravity

We develop a symmetric teleparallel gravity model in a space-time with only the non-metricity is nonzero, in terms of a Lagrangian quadratic in the non-metricity tensor. We present a detailed discussion of the variations that may be used for any gravitational formulation. We seek Schwarzschild-type solutions because of its observational significance and obtain a class of solutions that includes Schwarzschild-type, Schwarzschild-de Sitter-type and Reissner-Nordstr\"{o}m-type solutions for certain values of the parameters. We also discuss the physical relevance of these solutions.Comment: Corrected typos, Accepted for publication in IJMP-

Virtual Taxila: A Web-Accessible, Multi-User Virtual Environment (MUVE) of an Ancient Indian City

The Virtual Taxila project will develop a web-accessible, 3D, immersive, multi-user virtual environment (MUVE), where visitors will engage in situated, participatory learning about ancient Indian culture. The project will focus on the archaeological site of Taxila, the ancient capital of western Punjab and now an UNESCO World Heritage site located in Pakistan. Taxila was inhabited c. 500 BCE to c. 700 CE, but the project will model the city as it stood at circa 1 CE. The model will include both the city's tangible heritage (the built environment and the physical artifacts) and its intangible heritage (the people and their rituals, commercial transactions, and work activities). Virtual Taxila will create a "situated" community of practice, where visitors will be immersed in the historical context about which they learn. By logging in online, visitors will be able to interact with computer controlled characters that will act as guides, providing them with an insider's experience

Effects of disorder in location and size of fence barriers on molecular motion in cell membranes

The effect of disorder in the energetic heights and in the physical locations of fence barriers encountered by transmembrane molecules such as proteins and lipids in their motion in cell membranes is studied theoretically. The investigation takes as its starting point a recent analysis of a periodic system with constant distances between barriers and constant values of barrier heights, and employs effective medium theory to treat the disorder. The calculations make possible, in principle, the extraction of confinement parameters such as mean compartment sizes and mean intercompartmental transition rates from experimentally reported published observations. The analysis should be helpful both as an unusual application of effective medium theory and as an investigation of observed molecular movements in cell membranes.Comment: 9 pages, 5 figure

Symmetric Teleparallel Gravity: Some exact solutions and spinor couplings

In this paper we elaborate on the symmetric teleparallel gravity (STPG) written in a non-Riemannian spacetime with nonzero nonmetricity, but zero torsion and zero curvature. Firstly we give a prescription for obtaining the nonmetricity from the metric in a peculiar gauge. Then we state that under a novel prescription of parallel transportation of a tangent vector in this non-Riemannian geometry the autoparallel curves coincides with those of the Riemannian spacetimes. Subsequently we represent the symmetric teleparallel theory of gravity by the most general quadratic and parity conserving lagrangian with lagrange multipliers for vanishing torsion and curvature. We show that our lagrangian is equivalent to the Einstein-Hilbert lagrangian for certain values of coupling coefficients. Thus we arrive at calculating the field equations via independent variations. Then we obtain in turn conformal, spherically symmetric static, cosmological and pp-wave solutions exactly. Finally we discuss a minimal coupling of a spin-1/2 field to STPG.Comment: Accepted for publication in the International Journal of Modern Physics