Related papers: Single-Trajectory Bayesian Modeling Reveals Multi-…
In this paper, we study the asymptotic behavior of the number of crossings by a one-dimensional diffusion of a threshold where the process exhibits stickiness. We distinguish three types of crossings and show that to each type corresponds a…
Magnetic resonance imaging (MRI) is a vital diagnostic tool, but its inherently long acquisition times reduce clinical efficiency and patient comfort. Recent advancements in deep learning, particularly diffusion models, have improved…
Sequence modeling approaches have shown promising results in robot imitation learning. Recently, diffusion models have been adopted for behavioral cloning in a sequence modeling fashion, benefiting from their exceptional capabilities in…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a…
Estimating single-cell responses across various perturbations facilitates the identification of key genes and enhances drug screening, significantly boosting experimental efficiency. However, single-cell sequencing is a destructive process,…
We investigate single-particle diffusion in a two-state Langevin model where the friction coefficient randomly switches between low-friction (liquid-like) and high-friction (glassy-like) states. The dynamics are governed by the ratio…
DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent…
In this study we investigate the Percolation Hypothesis for Multiple Sclerosis Progression. The methodology relies on cross-reference analysis centered around a question: What is the evidence for a Percolation/phase-transition hypothesis in…
Anomalous diffusion phenomenon is an intriguing process that tracer diffusion presents in numerous complex systems. Current experimental and theoretical investigations have reported the emergence of random diffusivity scenarios accompanied…
DNA helicases are molecular motors that use the energy from ATP hydrolysis to move along DNA, promoting the unwinding or rewinding of the double helix. Here, we use magnetic and optical tweezers to track the motion of three helicases, gp41,…
Electrospinning is a highly sensitive fabrication process in which small variations in operating parameters can significantly influence fiber morphology and material performance. Machine learning (ML) methods are increasingly employed to…
Simulating trajectories of multi-particle systems on complex energy landscapes is a central task in molecular dynamics (MD) and drug discovery, but remains challenging at scale due to computationally expensive and long simulations. Previous…
Loop extrusion convincingly describes how certain Structural Maintenance of Chromosome (SMC) proteins mediate the formation of large DNA loops. Yet, most of the existing computational models cannot reconcile recent in vitro observations…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single molecule and single cell level can add…
Epidemic processes are common out-of-equilibrium phenomena of broad interdisciplinary interest. Recently, dynamic message-passing (DMP) has been proposed as an efficient algorithm for simulating epidemic models on networks, and in…
Measurements of protein motion in living cells and membranes consistently report transient anomalous diffusion (subdiffusion) which converges back to a Brownian motion with reduced diffusion coefficient at long times, after the anomalous…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
We study diffusion in ratchet systems. As a particular experimental realization we consider an asymmetric SQUID subjected to an external ac current and a constant magnetic flux. We analyze mean-square displacement of the Josephson phase and…
New ideas and technologies adopted by a small number of individuals occasionally spread globally through a complex web of social ties. Here, we present a simple and general approximation method, namely, a message-passing approach, that…