Related papers: A nucleotide-level coarse-grained model of RNA

We use a recently developed coarse-grained model to simulate the overstretching of duplex DNA. Overstretching at 23C occurs at 74 pN in the model, about 6-7 pN higher than the experimental value at equivalent salt conditions. Furthermore,…

Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done…

We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…

We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a `burnt-bridges' DNA motor consisting of a single-stranded cargo that steps processively…

The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon…

We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…

We introduce Coarse-Grained Nonlinear Dynamics, an efficient and universal parameterization of nonlinear system dynamics based on the Volterra series expansion. These models require a number of parameters only quasilinear in the system's…

RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…

Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…

The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…

We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA…

Simulating large proteins using traditional molecular dynamics (MD) is computationally demanding. To address this challenge, we propose a novel tree-structured coarse-grained model that efficiently captures protein dynamics. By leveraging a…

Biological systems exhibit processes on a wide range of time and length scales. This work demonstrates that models, wherein the interaction between system constituents is captured by algebraic operations, inherently allow for successive…

RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…

This dissertation explores how deep generative models can advance the analysis of challenging biological problems by integrating domain knowledge with deep learning. It focuses on two areas: DNA reaction kinetics and cryogenic electron…

We extend a renormalization group-based course-graining method for micromagnetic simulations to include properly scaled magnetostatic interactions. We apply the method in simulations of dynamic hysteresis loops at clinically relevant sweep…

We present a coarse-grained model for linear polymers with a tunable number of effective atoms (blobs) per chain interacting by intra- and inter-molecular potentials obtained at zero density. We show how this model is able to accurately…

We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…

Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains…

Much of our understanding of complex structures is based on simplification: for example, metal-organic frameworks are often discussed in the context of "nodes" and "linkers", allowing for a qualitative comparison with simpler inorganic…