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Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
A fundamental design rule that nature has developed for biological machines is the intimate correlation between motion and function. One class of biological machines is molecular motors in living cells, which directly convert chemical…
Loop formation in long molecules occurs many places in nature, from solutions of carbon nanotubes to polymers inside a cell. In this article, we review theoretical studies of the static and dynamic properties of polymer loops. For example,…
Biomolecular condensates have been shown to play a fundamental role in localizing biochemistry in a cell. RNA is a common constituent of condensates, and can determine their biophysical properties. Functions of biomolecular condensates are…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and…
Conventional kinesin is a homodimeric motor protein that unidirectionally transports organelles along filamentous microtubule (MT) by hydrolyzing ATP molecules. This study shows that the load modulations of ATP turnover and head diffusion…
Transcription is regulated through interplay between transcription factors, an RNA polymerase(RNAP), and a promoter. Even for a simple repressive transcription factor that disturbs promoter activity at the initial binding of RNAP, its…
Synthetic molecular motors are an appealing means to control motion at the nanoscale, but understanding their behaviour as single-molecule actuators and integrating them into larger, functional systems remain technical challenges.…
Gene transcription by a RNA Polymerase (RNAP) enzyme requires that double-stranded DNA be locally and transiently opened, which results in an increase of DNA supercoiling downstream of the RNAP and a decrease of supercoiling upstream of it.…
We investigate the voltage-driven transport of hybridized DNA through membrane channels. As membrane channels are typically too narrow to accommodate hybridized DNA, the dehybridization of the DNA is the critical rate limiting step in the…
ATP-dependent chromatin remodeling enzymes (CRE) are bio-molecular motors in eukaryotic cells. These are driven by a chemical fuel, namely, adenosine triphosphate (ATP). CREs actively participate in many cellular processes that require…
RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…
In many important cellular processes, including mRNA translation, gene transcription, phosphotransfer, and intracellular transport, biological "particles" move along some kind of "tracks". The motion of these particles can be modeled as a…
The effect of sequence heterogeneity on the dynamics of molecular motors is reviewed and analyzed using a set of recently introduced lattice models. First, we review results for the influence of heterogenous tracks such as a single-strand…
We have micromachined a silicon-chip device that transports DNA with a Brownian ratchet that rectifies the Brownian motion of microscopic particles. Transport properties for a DNA 50mer agree with theoretical predictions, and the DNA…
In fast growing bacteria, ribosomal RNA (rRNA) is required to be transcribed at very high rates to sustain the high cellular demand on ribosome synthesis. This results in dense traffic of RNA polymerases (RNAP). We developed a stochastic…
An inchworm processive mechanism is proposed to explain the motion of dimeric molecular motors such as kinesin. We present here preliminary results for this mechanism focusing on observables like mean velocity, coupling ratio and efficiency…
In recent literature there has been a lot of interest in the phenomena of noise induced transport in the absence of an average bias occurring in spatially periodic systems far from equilibrium. One of the main motivations in this area is to…