Related papers: Minimal Models for RNA Simulations
The complexity of biomolecular interactions necessitates advanced methodologies to accurately capture their behavior in solution. In this work, we focus on monoclonal antibodies and adopt a multi-scale coarse-graining strategy for their…
Phase separation, crucial for spatially segregating biomolecules in cells, is well-understood in the simple case of a few components with pairwise interactions. Yet, biological cells challenge the simple picture in at least two ways: First,…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
Cell cortex contraction is essential for shaping cells, enabling movement, ensuring proper division, maintaining tissue integrity, guiding development, and responding to mechanical signals - all critical for the life and health of…
Cross-protection, which refers to a process whereby artificially inoculating a plant with a mild strain provides protection against a more aggressive isolate of the virus, is known to be an effective tool of disease control in plants. In…
Folding of RNA is subject to a competition between entropy, relevant at high temperatures, and the random, or random looking, sequence, determining the low- temperature phase. It is known from numerical simulations that for random as well…
We build a simple model for feedback systems involving small RNA (sRNA) molecules based on the iron metabolism system in the bacterium E. coli, and compare it with the corresponding system in H. pylori which uses purely transcriptional…
Ion channels are of major interest and form an area of intensive research in the fields of biophysics and medicine since they control many vital physiological functions. The aim of this work is on one hand to propose a fully stochastic and…
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…
Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian…
Regulatory genes called small RNAs (sRNAs) are known to play critical roles in cellular responses to changing environments. For several sRNAs, regulation is effected by coupled stoichiometric degradation with messenger RNAs (mRNAs). The…
The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic…
We review the basic concepts and tools for mechanically unzipping RNA hairpins using force spectroscopy. By pulling apart the ends of an RNA molecule using optical tweezers, it is possible to measure the folding free energy at varying…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
RNA molecules in living cells form what look like liquid droplets formed by liquid/liquid phase separation. But unlike the molecules in conventional phase separating mixtures, RNA molecules are transported by molecular motors that consume…
During the lifecycle of many single-stranded RNA viruses, including many human pathogens, a protein shell called the capsid spontaneously assembles around the viral genome. Understanding the mechanisms by which capsid proteins selectively…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
Gene Regulatory Network (GRN) plays an important role in knowing insight of cellular life cycle. It gives information about at which different environmental conditions genes of particular interest get over expressed or under expressed.…
The dynamics of phase transitions plays a crucial r\^ole in the so-called interface between high energy particle physics and cosmology. Many of the interesting results generated during the last fifteen years or so rely on simplified…