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We report a study of DNA (150 bp fragments) conformations in very low added salt $<0.05$mM, across wide DNA concentration range $0.0015\leq c \leq 8$~mM (bp). We found an intermediate DNA conformation in the region $0.05 < c < 1$~mM, by…
This paper presents a numerical study of the dynamics of DNA double helix breakage under the influence of external forces using the Peyrard-Bishop-Dauxois (PBD) model. The PBD model represents DNA as a chain of nonlinearly coupled…
In eukaryotic cell nuclei, a variety of DNA interactions with nuclear elements occur, which, in combination with intra- and inter- chromosomal cross-talks, shape a functional 3D architecture. In some cases they are organized by active, i.e.…
A recent description of diffusion-limited nucleation based on fluctuating hydrodynamics that extends classical nucleation theory predicts a very non-classical two-step scenario whereby nucleation is most likely to occur in…
Knowledge of bubble and drop size distributions in two-phase flows is important for characterizing a wide range of phenomena, including combustor ignition, sonar communication, and cloud formation. The physical mechanisms driving the…
We consider two models of interacting DNA molecules: \textit{First} is (four parametric) bubble coalescence model in interacting DNAs (shortly: BCI-DNA). \textit{Second} is (three parametric) bubble coalescence model in a condensed DNA…
While many physics-based closure model forms have been posited for the sub-filter scale (SFS) in large eddy simulation (LES), vast amounts of data available from direct numerical simulation (DNS) create opportunities to leverage data-driven…
A probabilistic discrete model for 2D protein crystal growth is presented. This model takes into account the available space and can describe growing processes of different nature due to the versatility of its parameters which gives the…
Star formation is a multi-scale problem, and only global simulations that account for the connection from the molecular cloud scale gas flow to the accreting protostar can reflect the observed complexity of protostellar systems.…
Predictions of nuclear properties far from measured data are inherently imprecise because of uncertainties in our knowledge of nuclear forces and in our treatment of quantum many-body effects in strongly-interacting systems. While the model…
Post-translational modifications (PTMs) have vital roles in extending the functional diversity of proteins and as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a…
Statistical analysis of financial data most focused on testing the validity of Brownian motion (Bm). Analysis performed on several time series have shown deviation from the Bm hypothesis, that is at the base of the evaluation of many…
Recently-reported data suggest that bubble nucleation on surfaces with nano-sized features (cavities and posts) may occur close to the thermodynamic saturation temperature. However, according to the traditional theory of heterogeneous…
This paper presents BubbleID, a sophisticated deep learning architecture designed to comprehensively identify both static and dynamic attributes of bubbles within sequences of boiling images. By amalgamating segmentation powered by Mask…
In recent years, the segmentation of short molecular trajectories with varying diffusive properties has drawn particular attention of researchers, since it allows studying the dynamics of a particle. In the past decade, machine learning…
In the field of phase change phenomena, the lack of accessible and diverse datasets suitable for machine learning (ML) training poses a significant challenge. Existing experimental datasets are often restricted, with limited availability…
We study the inductive biases of diffusion models with a conditioning-variable, which have seen widespread application as both text-conditioned generative image models and observation-conditioned continuous control policies. We observe that…
We extend the phase field crystal model to accommodate exact atomic configurations and vacancies by requiring the order parameter to be non-negative. The resulting theory dictates the number of atoms and describes the motion of each of…
Change point detection plays a fundamental role in many real-world applications, where the goal is to analyze and monitor the behaviour of a data stream. In this paper, we study change detection in binary streams. To this end, we use a…
Most gas in giant molecular clouds is relatively low-density and forms star inefficiently, converting only a small fraction of its mass to stars per dynamical time. However, star formation models generally predict the existence of a…