Related papers: Modal Geometry Governs Proteoform Dynamics
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
The automorphism invariant theory of Crawford[J. Math. Phys. 35, 2701 (1994)] has show great promise, however its application is limited by the paradigm to the domain of spin space. Our conjecture is that there is a broader principle at…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
We perform an analytical investigation of the cell interface dynamics in the framework of a minimal phase field model of cell motility suggested in [1], which consists of two coupled evolution equations for the order parameter and a…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…
Given (small amounts of) time-series' data from a high-dimensional, fine-grained, multiscale dynamical system, we propose a generative framework for learning an effective, lower-dimensional, coarse-grained dynamical model that is predictive…
It has long been appreciated that transport properties can control reaction kinetics. This effect can be characterized by the time it takes a diffusing molecule to reach a target -- the first-passage time (FPT). Although essential to…
We construct a model of quantum gravity in which dimension, topology and geometry of spacetime are dynamical. The microscopic degree of freedom is a real rectangular matrix whose rows label internal flavours, and columns label spatial…
Understanding the geometry and topology of configuration or conformational spaces of molecules has relevant applications in chemistry and biology such as the proteins folding problem, drug design and the structure activity relationship…
Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it…
Understanding how transcription factors (TFs) regulate mammalian gene expression in space and time is a central topic in biology. To activate a gene, a TF has first to diffuse in the available space of the nucleus until it reaches a target…
This piece serves two purposes. Firstly, it aims at elucidating the role of epistasis in shaping, at a molecular level, the evolutionary paths of proteins, as well as the extent to which these epistatic effects are the outcome of an…
Morphoelasticity represents a foundational theory for tracing back growth, remodelling, and morphogenesis, yet crucial challenges persist. A unified growth law -- independent of a priori assumptions about constitutive relations or specified…
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…
In this essay, we wish to propose a general principle: \it{the equation of motion or dynamics of a fundamental force should not be prescribed but instead be entirely driven by geometry of the appropriate spacetime manifold, and the equation…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
A central aspect of the cosmological constant problem is to understand why vacuum energy does not gravitate. In order to account for this observation, while allowing for nontrivial dynamics of the quantum vacuum, we motivate a novel…
The field equations of a generalized $f(R)$ type gravity model, in which there is an arbitrary coupling between matter and geometry, are obtained. The equations of motion for test particles are derived from a variational principle in the…