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The complexity of mathematical models describing respiratory mechanics has grown in recent years to integrate with cardiovascular models and incorporate nonlinear dynamics. However, additional model complexity has rarely been studied in the…
We introduce topological methods for quantifying spatially heterogeneous dynamics, and use these tools to analyze particle-tracking data for a quasi-two-dimensional granular system of air-fluidized beads on approach to jamming. In…
It appears that thermally activated DNA bubbles of different sizes play central roles in important genetic processes. Here we show that the probability for the formation of such bubbles is regulated by the number of soft AT pairs in…
We investigate the relative phase coherence properties and the occurrence of demixing instabilities for two mutually interacting and time evolving Bose-Einstein condensates in traps. Our treatment naturally includes the additional…
We have managed to correlate the stability constants of complex formation, which can be registered in equilibrium state, to the dynamic characteristic of the complex lifetime. Thus, the principal concept of molecular biophysics regarding…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
We analyze thoroughly the mean-field dynamics of a linear chain of three coupled Bose-Einstein condensates, where both the tunneling and the central-well relative depth are adjustable parameters. Owing to its nonintegrability, entailing a…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can…
We study the properties of moving breathers in a bent DNA-related model with short range interaction, due to the stacking of the base pairs, and long range interaction, due to the finite dipole moment of the bonds within each base pair. We…
Single molecule probes are widely used to characterize dynamic heterogeneity in glass forming liquids, but interpreting probe dynamics remains challenging because the measured response depends on how the probe couples to its host…
Phase-separated biomolecular condensates exhibit a wide range of dynamical properties, which depend on the sequences of the constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of…
The Poland--Scheraga model, introduced in the 1970's, is a reference model to describe the denaturation transition of DNA. More recently, it has been generalized in order to allow for asymmetry in the strands lengths and in the formation of…
The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to…
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe…
A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The…