Related papers: Minimal Models for RNA Simulations
Finding coarse-grained, low-dimensional descriptions is an important task in the analysis of complex, stochastic models of gene regulatory networks. This task involves (a) identifying observables that best describe the state of these…
The processes, resulting in the transcription of RNA, are intrinsically noisy. It was observed experimentally that the synthesis of mRNA molecules is driven by short, burst-like, events. An accurate prediction of the protein level often…
We summarize the recent simulation progress of micromanipulation experiments on RNAs. Our work mainly consults with two important small RNAs unfolding experiments carried out by Bustamante group. Our results show that, in contrast to…
Because of the potential link between -1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed…
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Due to the limitation of the previous database, especially…
We develop a coarse-grained protein model with a simplified amino acid interaction potential. We perform discrete molecular dynamics folding simulations of a small 20 residue protein - Trp-cage - from a fully extended conformation. We…
Calcium and reactive oxygen species (ROS) interact with each other and play an important role in cell signaling networks. Based on the existing mathematical models, we develop an age-dependent feedback control model to simulate the…
In line with the importance of RNA-seq, the bioinformatics community has produced numerous data analysis tools incorporating methods to correct sample-specific biases. However, few advanced simulation tools exist to enable benchmarking of…
There is a pressing need for a description of complex systems that includes considerations of the underlying network of interactions, for a diverse range of biological, technological and other networks. In this work relationships between…
Energy functions for pure and heterogenous systems are one of the backbones for molecular simulation of condensed phase systems. With the advent of machine learned potential energy surfaces (ML-PESs) a new era has started. Statistical…
Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA…
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 study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
The prediction of the equation of state and the phase behavior of simple fluids (noble gases, carbon dioxide, benzene, methane, short alkane chains) and their mixtures by Monte Carlo computer simulation and analytic approximations based on…
Phase separation in biomolecular mixtures can result from multiple physical interactions, which may act either complementarily or antagonistically. In the case of protein-nucleic acid mixtures, charge plays a key role but can have…
Folding of ribozymes into well-defined tertiary structures usually requires divalent cations. How Mg$^{2+}$ ions direct the folding kinetics has been a long-standing unsolved problem because experiments cannot detect the positions and…