Related papers: Compound Poisson Statistics and Models of Clusteri…
Data poisoning is one of the most relevant security threats against machine learning and data-driven technologies. Since many applications rely on untrusted training data, an attacker can easily craft malicious samples and inject them into…
The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybridization rates by factors of 2 and 10 respectively, in good…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
The paper introduces the concept of a cluster structure to define a joint distribution of the sample size and its exchangeable random partitions. The cluster structure allows the probability distribution of the random partitions of a subset…
While state-of-the-art diffusion models (DMs) excel in image generation, concerns regarding their security persist. Earlier research highlighted DMs' vulnerability to data poisoning attacks, but these studies placed stricter requirements…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
A model of arsenic clustering in silicon is proposed and analyzed. The main feature of the proposed model is the assumption that negatively charged arsenic complexes play a dominant role in the clustering process. To confirm this…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
Poisoning-based backdoor attacks pose significant threats to deep neural networks by embedding triggers in training data, causing models to misclassify triggered inputs as adversary-specified labels while maintaining performance on clean…
The ability of double-stranded DNA or RNA to locally melt and form kinks leads to strong non-linear elasticity effects that qualitatively affect their packing in confined spaces. Using analytical theory and numerical simulation we show that…
Model-based clustering is widely-used in a variety of application areas. However, fundamental concerns remain about robustness. In particular, results can be sensitive to the choice of kernel representing the within-cluster data density.…
We consider the influence of a terahertz field on the breathing dynamics of double-stranded DNA. We model the spontaneous formation of spatially localized openings of a damped and driven DNA chain, and find that linear instabilities lead to…
Clustering is one of the most complex phenomena known to the structure of atomic nuclei. A comprehensive description of this ubiquitous phenomenon goes beyond standard shell model and cluster model frameworks. We argue that clustering is a…
We study numerically a disordered version of the model for DNA denaturation transition (DSAW-DNA) consisting of two interacting SAWs in 3d, which undergoes a first order transition in the homogeneous case. The two possible values eAT and…
The theoretical approach to a sequential heavy ion double charge exchange reaction is presented. A brief introduction into the formal theory of second-order nuclear reactions and their application to Double Single Charge Exchange (DSCE)…
We propose an inclusive approach for calculating characteristics of secondary electrons produced by ions/protons in tissue-like media. This approach is based on an analysis of the projectile's interaction with the medium on the microscopic…