Related papers: Structure-Function Dynamics Hybrid Modeling: RNA D…
MicroRNAs (miRNAs) critically modulate stem cell properties like pluripotency, but the fundamental mechanism remains largely unknown. This study systematically analyzes multiple-omics data and builds a systems physical network including…
Aging is a fundamental aspect of living systems that undergo a progressive deterioration of physiological function with age and an increase of vulnerability to disease and death. Living systems, known as complex systems, require complexity…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
Bioprocess mechanistic modeling is essential for advancing intelligent digital twin representation of biomanufacturing, yet challenges persist due to complex intracellular regulation, stochastic system behavior, and limited experimental…
A central challenge in modeling neurodegenerative diseases is connecting cellular-level mechanisms to tissue-level pathology, in particular to determine whether pathology is driven primarily by cell-autonomous triggers or by propagation…
The interaction of phase-separating systems with chemical reactions is of great interest in various contexts, from biology to material science. In biology, phase separation is thought to be the driving force behind the formation of…
In this paper we model several simple biochemical operations on RNA molecules that modify their secondary structure by means of a suitable variation of Gro\ss e-Rhode's Algebra Transformation Systems.
Dynamic recrystallization is one of the main phenomena responsible for microstructure evolutions during hot forming. Consequently, getting a better understanding of DRX mechanisms and being able to predict them is crucial. This paper…
Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that…
RNAs are negatively charged molecules residing in macromolecular crowding cellular environments. Macromolecular confinement can influence the ion effects in RNA folding. In this work, using the recently developed tightly bound ion model for…
In exploring the simulation of human rhythmic perception and synchronization capabilities, this study introduces a computational model inspired by the physical and biological processes underlying rhythm processing. Utilizing a reservoir…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
There is a growing body of work considering the use of representations based upon genetic regulatory networks. This paper uses a recently presented abstract, tunable Boolean regulatory network model to explore aspects of mobile DNA, such as…
The challenge of translating vast, multimodal biological data into predictive and mechanistic understanding of cellular function is a central theme in modern biology. Virtual cells, or digital cellular twins, have emerged as a critical…
In this paper, we use the biological domain knowledge incorporated into stochastic models for ab initio RNA secondary-structure prediction to improve the state of the art in joint compression of RNA sequence and structure data (Liu et al.,…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
This work presents RNAdiffusion, a latent diffusion model for generating and optimizing discrete RNA sequences of variable lengths. RNA is a key intermediary between DNA and protein, exhibiting high sequence diversity and complex…
Reduced-order models that accurately abstract high fidelity models and enable faster simulation is vital for real-time, model-based diagnosis applications. In this paper, we outline a novel hybrid modeling approach that combines machine…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…