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While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
A double-stranded DNA unravels thermally through intermediate denatured bubble segments. Intrinsically, fluctuations ensue at the bubble boundaries from non-equilibrium (NE) energy exchanges with the environment. However, such details gets…
The spontaneous formation of tiny bubbles in a liquid is at the root of the nucleation mechanism during the liquid-to-vapor transition of a metastable liquid. The smaller the bubbles the larger their probability to appear, and even for…
Modeling boiling (an inherently chaotic, multiphase process central to energy and thermal systems) remains a significant challenge for neural PDE surrogates. Existing models require future input (e.g., bubble positions) during inference…
We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the…
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…
Reasoning distillation has emerged as a prevailing paradigm for transferring reasoning capabilities from large reasoning models to small language models. Yet, reasoning distillation risks data contamination: benchmark data may inadvertently…
In the framework of the Polyakov quark-meson model with two flavors, the bubble dynamics of a first-order phase transition in the region of high density and low temperature are investigated by using the homogeneous thermal nucleation…
Diffusion-based posterior samplers use pretrained diffusion priors to sample from measurement- or reward-conditioned posteriors, and are widely used for inverse problems. Yet their theoretical behavior remains poorly understood: even with…
A nonperturbative correction to the thermal nucleation rate of critical bubbles in a first order phase transition is estimated. The correction originates from large-amplitude fluctuations which may be present before the transition occurs.…
In the demanding biosensing environment, improving selection efficiency strategies has become an issue of great significance. DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, are representative of the…
Pattern formation in biological tissues plays an important role in the development of living organisms. Since the classical work of Alan Turing, a pre-eminent way of modelling has been through reaction-diffusion mechanisms. More recently,…
Phase-averaged dilute bubbly flow models require high-order statistical moments of the bubble population. The method of classes, which directly evolve bins of bubbles in the probability space, are accurate but computationally expensive.…
We present an analysis of late-O/early-B-powered, parsec-sized bubbles and associated star-formation using 2MASS, GLIMPSE, MIPSGAL and MAGPIS surveys. Three bubbles were selected from the Churchwell et al. (2007) catalog. We confirm that…
The process of nucleation of vapor bubbles from a superheated liquid and of liquid droplets from a supersaturated vapor is investigated using the Modified-Core van der Waals model Density Functional Theory (Lutsko, JCP 128, 184711 (2008)).…
Multiphase fluid dynamics, such as falling droplets and rising bubbles, are critical to many industrial applications. However, simulating these phenomena efficiently is challenging due to the complexity of instabilities, wave patterns, and…
This article demonstrates that flexible and statistically tractable multi-modal diffusion models can be attained by transformation of simple well-known diffusion models such as the Ornstein-Uhlenbeck model, or more generally a Pearson…
This paper is a sequel of the 2019 paper [5]. It demonstrates the following: a) the Poisson multi-Bernoulli mixture (PMBM) approach to detected vs. undetected (U/D) targets cannot be rigorously formulated using either the two-step or…
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…
The Peyrard-Bishop DNA model describes the molecular interactions with simple potentials which allow efficient calculations of melting temperatures. However, it is based on a Hamiltonian that does not consider the helical twist or any other…