相关论文: Stepwise bending of DNA by a single TATA-box Bindi…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four…
RNA polymerase (RNAP) elongates RNA by walking along a DNA template and selectively incorporating ribonucleoside triphosphates (rNTPs). Rather than mechanically replicating the base sequence, RNAP conditions binding and chemistry on the…
A DNA polymerase (DNAP) replicates a template DNA strand. It also exploits the template as the track for its own motor-like mechanical movement. In the polymerase mode it elongates the nascent DNA by one nucleotide in each step. But,…
We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account…
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 tandem cell is proposed for DNA sequencing in which an exonuclease enzyme cleaves bases (mononucleotides) from a strand of DNA for identification inside a nanopore. It has two nanopores and three compartments with the structure [cis1,…
Extracting the intrinsic kinetic information of biological molecule from its single-molecule kinetic data is of considerable biophysical interest. In this work, we theoretically investigate the feasibility of inferring single RNA's…
Protein allostery requires dynamical structural correlations. Physical origin of which, however, remain elusive despite intensive studies during last two decades. Based on analysis of molecular dynamics (MD) simulation trajectories for ten…
Active transport of biomolecular condensates and cell migration in collectives are fundamental to development, homeostasis, and processes such as cancer progression, wound healing, and infection response. Yet how these assemblies are…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such…
Membrane phase behavior induced by the binding of curvature-inducing proteins is studied by a combination of analytical and numerical approaches. In thermal equilibrium under the detailed balance between binding and unbinding, the membrane…
DNA flexibility is a key determinant of biological function, from nucleosome positioning to transcriptional regulation, motivating a direct measurement of the bend-torque response of individual DNA molecules. In this work, DNA bending is…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
Subcellular protein complexes and organelles exhibit diverse dynamic behaviors that reflect the mechanical constraints and organization of the intracellular environment. Although some structures follow classical Brownian motion, many…
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such…
Using a theoretical model for spontaneous partial DNA unwrapping from histones, we study the transient exposure of protein-binding DNA sites within nucleosomes. We focus on the functional dependence of the rates for site exposure and…
We study the tautomeric transitions in base pairs of DNA considering elastic properties of DNA as classical and tunneling of protons as quantum, and show that the dynamics of the transitions admits of soliton like solutions whose shape and…
We use a three dimensional cubic lattice model of proteins to study their properties that determine folding to the native state. The protein chain is modeled as a sequence of $N$ beads. The interactions between beads are taken from a…