Related papers: Exploring RNA structure and dynamics through enhan…
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
Despite the accelerating presence of exploratory causal analysis in modern science and medicine, the available non-experimental methods for validating causal models are not well characterized. One of the most popular methods is to evaluate…
This paper presents a SysML-based approach to enhance functional and software development process within an industrial context. The recent changes in technology such as electromobility and increased automation in heavy construction…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
The ability of a cell to communicate with its environment is essential for key cellular functions like replication, metabolism, or cell fate decisions. The involved molecular mechanisms are highly dynamic and difficult to capture…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
In this paper, we propose applying semantic embedding to learn the range of behaviors exhibited by molecular swarms, thereby providing a richer set of features to optimize such systems. Specifically, we consider a standard molecular swarm…
Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible binding sites for Mg$^{2+}$ on a RNA duplex, including both…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
Causal discovery can be a powerful tool for investigating causality when a system can be observed but is inaccessible to experiments in practice. Despite this, it is rarely used in any scientific or medical fields. One of the major hurdles…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
Efficient sampling in biomolecular simulations is critical for accurately capturing the complex dynamical behaviors of biological systems. Adaptive sampling techniques aim to improve efficiency by focusing computational resources on the…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…