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We investigate a model of chaperone-assisted polymer translocation through a nanopore in a membrane. Translocation is driven by irreversible random sequential absorption of chaperone proteins that bind to the polymer on one side of the…

Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called ribosomes. Although the experimental investigation of protein synthesis has been a traditional area of research in molecular cell…

Recent research has emphasized the benefits of accurately reconstructing the initial Lagrangian positions of biased tracers from their positions at a later time, to gain cosmological information. A weighted semi-discrete optimal transport…

Many crucial biological processes rely on networks of protein-protein interactions. Predicting the effect of amino acid mutations on protein-protein binding is vital in protein engineering and therapeutic discovery. However, the scarcity of…

We propose a dissipative electro-elastic network model (DENM) to describe the dynamics and statistics of electrostatic fluctuations at active sites of proteins. The model combines the harmonic network of residue beads with overdamped…

We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to…

Cell migration is a fundamental process involved in physiological phenomena such as the immune response and morphogenesis, but also in pathological processes, such as the development of tumor metastasis. These functions are effectively…

Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the…

Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…

This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the…

How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…

Stochastic resetting is prevalent in natural and man-made systems giving rise to a long series of non-equilibrium phenomena. Diffusion with stochastic resetting serves as a paradigmatic model to study these phenomena, but the lack of a…

The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…

This work introduces the generative fractional diffusion model for protein generation (ProT-GFDM), a novel generative framework that employs fractional stochastic dynamics for protein backbone structure modeling. This approach builds on the…

Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…

We study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition path theory we…

We study forward and inverse problems for a semilinear radiative transport model where the absorption coefficient depends on the angular average of the transport solution. Our first result is the well-posedness theory for the transport…

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…

Intracellular transport of large cargoes, such as organelles, vesicles or large proteins, is a complex dynamical process that involves the interplay of ATP-consuming molecular motors, cytoskeleton filaments and the viscoelastic cytoplasm.…

A cell is polarised when it has developed a main axis of organisation through the reorganisation of its cytosqueleton and its intracellular organelles. Polarisation can occur spontaneously or be triggered by external signals, like gradients…