Related papers: Structure-Function Dynamics Hybrid Modeling: RNA D…

This paper proposes a neural network hybrid modeling framework for dynamics learning to promote an interpretable, computationally efficient way of dynamics learning and system identification. First, a low-level model will be trained to…

This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…

Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA that target specific ligands face limitations in capturing…

DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA…

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…

The fundamental biological processes of development of tissues and organs in multicellular organisms is governed by various signaling molecules, which are called morphogens. It is known that spatial and temporal variations in concentration…

RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…

Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…

Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…

Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have…

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…

This paper establishes a general framework for describing hybrid dynamical systems which is particularly suitable for numerical simulation. In this context, the data structures used to describe the sets and functions which comprise the…

Degeneration and adaptation are two competing sides of the same coin called resilience in the progressive processes of brain aging or diseases. Degeneration accumulates during brain aging and other cerebral activities, causing structural…

Bio-hybrid systems---close couplings of natural organisms with technology---are high potential and still underexplored. In existing work, robots have mostly influenced group behaviors of animals. We explore the possibilities of mixing…

We view the folding of RNA-sequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure…

Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…

Emerging evidence suggests that the introns and intergenic sequences of the genomes of higher eukaryotes (the ``junk'' DNA) codes for a vast, RNA-based, genetic regulatory network. It is believed that this network is responsible for the…

Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical…

Models play an essential role in the design process of cyber-physical systems. They form the basis for simulation and analysis and help in identifying design problems as early as possible. However, the construction of models that comprise…