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Backtracking of RNA polymerase (RNAP) is an important pausing mechanism during DNA transcription that is part of the error correction process that enhances transcription fidelity. We model the backtracking mechanism of RNA polymerase, which…
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
Polymerization of RNA from a template DNA is carried out by a molecular machine called RNA polymerase (RNAP). It also uses the template as a track on which it moves as a motor utilizing chemical energy input. The time it spends at each…
In this work, we propose a simple transformer-based baseline for multimodal molecular representation learning, integrating three distinct modalities: SMILES strings, 2D graph representations, and 3D conformers of molecules. A key aspect of…
In multi-source sequence-to-sequence tasks, the attention mechanism can be modeled in several ways. This topic has been thoroughly studied on recurrent architectures. In this paper, we extend the previous work to the encoder-decoder…
Designing components that can robustly self-assemble into structures with biological complexity is a grand challenge for material science. Proofreading and error correction is required to improve assembly yield beyond equilibrium limits,…
Multimodal molecular representation learning, which jointly models molecular graphs and their textual descriptions, enhances predictive accuracy and interpretability by enabling more robust and reliable predictions of drug toxicity,…
Polymers, composed of repeating structural units called monomers, are fundamental materials in daily life and industry. Accurate property prediction for polymers is essential for their design, development, and application. However, existing…
The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…
Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently…
We propose a new and fully end-to-end approach for multimodal translation where the source text encoder modulates the entire visual input processing using conditional batch normalization, in order to compute the most informative image…
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…
Manipulation tasks often consist of subtasks, each representing a distinct skill. Mastering these skills is essential for robots, as it enhances their autonomy, efficiency, adaptability, and ability to work in their environment. Learning…
Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…
In recent years, a myriad of advanced results have been reported in the community of imitation learning, ranging from parametric to non-parametric, probabilistic to non-probabilistic and Bayesian to frequentist approaches. Meanwhile, ample…
We present a calculation technique for modeling inhomogeneous DNA replication kinetics, where replication factors such as initiation rates or fork speeds can change with both position and time. We can use our model to simulate data sets…
Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as…
The adsorption of an ideal heteropolymer loop at a potential point well is investigated within the frameworks of a standard random matrix theory. On the basis of semi-analytical/semi-numerical approach the histogram of transition points for…
Translation is an important process for prokaryotic and eukaryotic cells to produce necessary proteins for cell growth. Numerious experiments have been performed to explore the translational properties. Diverse models have also been…