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De novo molecular generation is an essential task for science discovery. Recently, fragment-based deep generative models have attracted much research attention due to their flexibility in generating novel molecules based on existing…
Synthetic biology aims at designing modular genetic circuits that can be assembled according to the desired function. When embedded in a cell, a circuit module becomes a small subnetwork within a larger environmental network, and its…
RNA in extant biological systems is homochiral; it consists exclusively of D-ribonucleotides rather than L-ribonucleotides. How the homochirality of RNA emerged is not known. Here, we use stochastic simulations to quantitatively explore the…
RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
We present a scenario for the origin of biological coding. In this context, coding is a semiotic relationship between chemical information stored in one location that links to chemical information stored in a separate location. Coding…
Any search for present or past life beyond Earth should consider the initial processes and related environmental controls that might have led to its start. As on Earth, such an understanding lies well beyond how simple organic molecules…
The interaction of phase-separating systems with chemical reactions is of great interest in various contexts, from biology to material science. In biology, phase separation is thought to be the driving force behind the formation of…
Networks are widely used in science and technology to represent relationships between entities, such as social or ecological links between organisms, enzymatic interactions in metabolic systems, or computer infrastructure. Statistical…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
The sequence of nucleotide bases occurring in an organism's DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical…
Background. Dramatic increases in RNA structural data have made it possible to recognize its conformational preferences much better than a decade ago. This has created an opportunity to use discrete restraint-based conformational sampling…
Test-time compute is central to large reasoning models, yet analysing their reasoning behaviour through generated text is increasingly impractical and unreliable. Response length is often used as a brute proxy for reasoning effort, but this…
Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees…
The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the…
Life can be viewed as a localized chemical system that sits on, or in the basin of attraction of, a metastable dynamical attractor state that remains out of equilibrium with the environment. Such a view of life allows that new living states…
RNA-Seq is a widely-used method for studying the behavior of genes under different biological conditions. An essential step in an RNA-Seq study is normalization, in which raw data are adjusted to account for factors that prevent direct…
Nuclei are unique analyzers for the early stage of the space-time development of hadronization. DIS at medium energies is especially suitable for this task being sensitive to hadronization dynamics, since the production length is comparable…
Protein synthesis is one of the most fundamental biological processes, which consumes a significant amount of cellular resources. Despite existence of multiple mathematical models of translation, varying in the level of mechanistical…
The origin of life is often approached through the lens of replication, heredity, or molecular specificity. This paper proposes a thermodynamic framework in which the emergence of life is driven by the persistence of reaction pathways that…