Related papers: FRETtranslator: translating FRET traces into RNA s…
Using a combination of theory and computer simulations, we study the translocation of an RNA molecule, pulled through a solid-state nanopore by an optical tweezer, as a method to determine its secondary structure. The resolution with which…
Understanding how 5' untranslated regions (5'UTRs) regulate mRNA translation is critical for controlling protein expression and designing effective therapeutic mRNAs. While recent deep learning models have shown promise in predicting…
Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…
Motivated by recent experiments on photon statistics from individual dye pairs planted on biomolecules and coupled by fluorescence resonance energy transfer (FRET), we show here that the FRET dynamics can be modelled by Gaussian random…
An experimental strategy has been developed specifically for the study of composition-dependent phase behavior in multi-component artificial membranes. The strategy is based on steady-state measurements of fluorescence resonance energy…
F\"{o}rster Resonance Energy Transfer Calculator (FRET$-$Calc) is a program and web server that analyzes molar extinction coefficient of the acceptor, emission spectrum of the donor, and the refractive index spectrum of the donor/acceptor…
A theory of electrical transport through molecular wires is used to estimate the electronic factor in the intramolecular electron transfer (ET) in porphyrin-nitrobenzene supermolecules, and to analyze its structure. The chosen molecules…
We present a first-principles calculation on the rate and efficiency of F\"orster resonance energy transfer (FRET) from a donor to an acceptor when they are located in the hotspots of nanoparticle clusters. Nonlocal effect has been…
Resonance frequencies can provide useful information on the deformation occurring during fracturing experiments or $CO_2$ management, complementary to the microseismic event distribution. An accurate time-frequency representation is of…
Inferring gene regulatory networks (GRNs) from single-cell RNA sequencing (scRNA-seq) data is a complex challenge that requires capturing the intricate relationships between genes and their regulatory interactions. In this study, we tackle…
We introduce a general framework to study dipole-dipole energy transfer between an emitter and an absorber in a nanostructured environment. The theory allows us to address F\"orster Resonant Energy Transfer (FRET) between a donor and an…
Temporally modulated metamaterials have attracted significant attention recently due to their non-reciprocal and frequency converting properties. Here, a transparent, time-modulated metasurface that functions as a serrodyne frequency…
Single-cell RNA sequencing (scRNA-seq) offers detailed insights into cellular heterogeneity. Recent advancements leverage single-cell large language models (scLLMs) for effective representation learning. These models focus exclusively on…
We study the F\"orster resonant energy transfer (FRET) rate in multichromophoric systems. The multichromophoric FRET rate is determined by the overlap integral of the donor's emission and acceptor's absorption spectra, which are obtained…
We have studied the influence of the local density of optical states (LDOS) on the rate and efficiency of Forster resonance energy transfer (FRET) from a donor to an acceptor. The donors and acceptors are dye molecules that are separated by…
Resonant Energy Transfer (RET) from an optically excited donor molecule (D) to a non-excited acceptor molecule (A) residing nearby is widely used to detect molecular interactions in living cells. Stoichiometric information, such as the…
Single-molecule approaches to biology offer a powerful new vision to elucidate the mechanisms that underpin the functioning of living cells. However, conventional optical single molecule spectroscopy techniques such as F\"orster…
Despite their widespread use in cell biology, fluorescence lifetime imaging microscopy (FLIM) data-sets are challenging to analyse, because each spatial position can contain a superposition of multiple fluorescent components. Here, we…
By circumventing the optical diffraction limit, super-resolved fluorescence microscopies enable the study of larger cellular structures and molecular assemblies. However, fluorescence nanoscopy currently lacks the spatiotemporal resolution…
Over the past 15 years there has been an ongoing debate regarding the influence of the photonic environment on Forster resonance energy transfer (FRET). Disparate results corresponding to enhancement, suppression and null effect of the…