Related papers: Coarse Graining RNA Nanostructures for Molecular D…
We discuss how simulations of mechanical properties of materials require descriptions at many different length scales --- from the nanoscale where an atomic description is appropriate, through a mesoscale where dislocation based…
In this work, we review previously developed coarse-grained (CG) particle models for biological membrane and red blood cells (RBCs) and discuss the advantages of the CG particle method over the continuum and atomic simulations on modeling…
In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
We establish, through coarse-grained computation, a connection between traditional, continuum numerical algorithms (initial value problems as well as fixed point algorithms) and atomistic simulations of the Larson model of micelle…
This paper presents a molecular mechanics study for new nanorobotic structures using molecular dynamics (MD) simulations coupled to virtual reality (VR) techniques. The operator can design and characterize through molecular dynamics…
Coarse-grained (CG) force field methods for molecular systems are a crucial tool to simulate large biological macromolecules and are therefore essential for characterisations of biomolecular systems. While state-of-the-art deep learning…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…
Studying the conformations involved in the dimerization of cadherins is highly relevant to understand the development of tissue and its failure, which is associated with tumors and metastases. Experimental techniques, like X-ray…
Stochastic modelling of complex systems plays an essential, yet often computationally intensive role across the quantitative sciences. Recent advances in quantum information processing have elucidated the potential for quantum simulators to…
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions. Additionally, artificially modified RNAs have been suggested…
A general scheme, which includes constructions of coarse-grained (CG) models, weighted ensemble dynamics (WED) simulations and cluster analyses (CA) of stable states, is presented to detect dynamical and thermodynamical properties in…
To study materials phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels, are necessary. Attempts to do this in the static regime (i.e. zero temperature) have already been…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…
Hierarchical biomaterials embody nature's intricate design principles, offering advanced functionalities through the complex, multi-level organization of their molecular and nanosized building blocks. However, the comprehensive…
Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics…
We report on a molecular dynamics investigation of the wetting properties of graphitic surfaces by various solutions at concentrations 1-8 wt% of commercially available non-ionic surfactants with long hydrophilic chains, linear or T-shaped.…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
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…