Related papers: Error-speed correlations in biopolymer synthesis
We study the spontaneous nucleation and crystallization of linear and cyclic chains of flexibly connected hard spheres using extensive molecular dynamics simulations. To this end, we present a novel event-driven molecular dynamics…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
A new method based on quasi-independent parallel simulations approach, replica-averaging, has been developed to study the influence of flow on mechanical force-mediated polymer processes such as denaturation and breaking of bonds. This…
We present predictions for the statistical error due to finite sampling in the presence of thermal fluctuations in molecular simulation algorithms. Specifically, we establish how these errors depend on Mach number, Knudsen number, number of…
Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs).…
Effective and fast convergence toward an equilibrium state for long-chain polymer melts is realized by a hybrid method coupling molecular dynamics and the elastic continuum. The required simulation time to achieve the equilibrium state is…
Polymer translocation is a promising strategy for the next-generation DNA sequencing technologies. The use of biological and synthetic nano-pores, however, still suffers from serious drawbacks. In particular, the width of the membrane layer…
Cell dynamics simulation is used to investigate the phase behavior of block copolymer/homopolymer mixture subjected to a steady shear flow. Phase transitions occur from transverse to parallel and then to perpendicular lamellar structure…
We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant…
In this work, we consider diffusion-based molecular communication with and without drift between two static nano-machines. We employ type-based information encoding, releasing a single molecule per information bit. At the receiver, we…
Biological polymers, such as intrinsically disordered proteins, play a central role in cellular biology, including mediating phase separation and controlling activity of biological condensates. The physical properties and functions of…
Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called RNA polymerase, which erratically moves along and scans the DNA template. We perform Bayesian inference…
We consider biochemical reaction chains and investigate how random external fluctuations, as characterized by variance and coefficient of variation, propagate down the chains. We perform such a study under the assumption that the number of…
The difference Delta F between free energies has applications in biology, chemistry, and pharmacology. The value of Delta F can be estimated from experiments or simulations, via fluctuation theorems developed in statistical mechanics.…
Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…
Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the…
Recent fluorescence spectroscopy measurements of the turnover time distribution of single-enzyme turnover kinetics of $\beta$-galactosidase provide evidence of Michaelis-Menten kinetics at low substrate concentration. However, at high…
We derive statistical-mechanical speed limits on dissipation from the classical, chaotic dynamics of many-particle systems. In one, the rate of irreversible entropy production in the environment is the maximum speed of a deterministic…
Phase aberrations, despite degrading ultrasound images, also encode valuable information about the spatial distribution of the speed of sound in tissue. In pulse-echo ultrasound, we can quantify them by exploiting speckle correlations.…
Standard library implementations of functions like sin and exp optimize for accuracy, not speed, because they are intended for general-purpose use. But applications tolerate inaccuracy from cancellation, rounding error, and…