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The activation/repression of a given gene is typically regulated by multiple transcription factors (TFs) that bind at the gene regulatory region and recruit RNA polymerase (RNAP). The interactions between the promoter region and TFs and…
Life on earth is distinguished by long-lived correlations in time. The patterns of material organization that characterize living organisms today are contingent on events that occurred billions of years ago. This contingency is a necessary…
In the study of grain-surface chemistry in the interstellar medium, there exists much uncertainty regarding the reaction mechanisms with few constraints on the abundances of grain-surface molecules. Bayesian inference can be performed to…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are…
A general Bayesian framework for model selection on random network models regarding their features is considered. The goal is to develop a principle Bayesian model selection approach to compare different fittable, not necessarily nested,…
Many biological systems dynamically rearrange their components through a sequence of configurations in order to perform their functions. Such dynamic processes have been studied using network models that sequentially retrieve a set of…
RNA interference (RNAi) is an endogenous cellular process in which small double-stranded RNAs lead to the destruction of mRNAs with complementary nucleoside sequence. With the production of RNAi libraries, large-scale RNAi screening in…
We implement the Bayesian inference to retrieve energy spectra of all neutrinos from a galactic core-collapse supernova (CCSN). To achieve high statistics and full sensitivity to all flavours of neutrinos, we adopt a combination of several…
Living cells exhibit a complex organization comprising numerous compartments, among which are RNA- and protein-rich membraneless, liquid-like organelles known as biomolecular condensates. Energy-consuming processes regulate their formation…
Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time…
The dynamics of gene transcription is tightly regulated in eukaryotes. Recent experiments have revealed various kinds of transcriptional dynamics, such as RNA polymerase II pausing, that involves regulation at the transcription initiation…
Bayesian Inference is a powerful approach to data analysis that is based almost entirely on probability theory. In this approach, probabilities model {\it uncertainty} rather than randomness or variability. This thesis is composed of a…
Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…
This work examines a field theory for RNA-like molecules in a good solvent. The field theory is based on a lattice model for single- and double-strand RNA with a periodic base sequence, and otherwise contains all known relevant details…
Nonlinear dynamics of photoinduced cooperative phenomena is studied by numerical calculations on a model of molecular crystals. We found that the photoinduced nucleation process is triggered only when certain amount of excitation energy is…
Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small…
We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…
In this paper, we present a neuro-inspired approach to reservoir computing (RC) in which a network of in vitro cultured cortical neurons serves as the physical reservoir. Rather than relying on artificial recurrent models to approximate…
In the event of a nuclear accident, or the detonation of a radiological dispersal device, quickly locating the source of the accident or blast is important for emergency response and environmental decontamination. At a specified time after…