Related papers: Regional compartmentalization in multienzyme-relat…
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,…
Field induced assembly of reconfigurable structures with complex hierarchical configurations has recently become an area of intense research with the promise for exciting applications in programmable self-assembly and nano/microstructure…
Living systems are made of active materials with microscopic components that work together to perform macroscopic biological tasks. The breakdown of these collective functionalities leads to diseases, which, conversely, could be treated by…
The need to harmonise apparently irreconcilable arrangements in an ecosystem --nestedness and segregation-- has triggered so far different strategies. Methodological refinements, or the inclusion of behavioural preferences to the network…
Causal structure discovery (CSD) models are making inroads into several domains, including Earth system sciences. Their widespread adaptation is however hampered by the fact that the resulting models often do not take into account the…
Unravelling current complex food systems is relevant for their adjustment and redesign under the current changing climate conditions. Redesign may be necessitated by migration of people and changes of locations of major agri-food…
Microplastics contamination is one of the most rapidly growing research topics. However, monitoring microplastics contamination in the environment presents both logistical and statistical challenges, particularly when constrained resources…
Biomolecular condensates are liquid- or gel-like droplets of proteins and nucleic acids formed at least in part through liquid-liquid phase separation. Condensates enable diverse functions of cells and the pathogens that infect them,…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
We present a general embedding theory of electronic excitations of a relatively small, localized system in contact with an extended, chemically complex environment. We demonstrate how to include the screening response of the environment…
Scaling the number of entangled nodes in a quantum network is a challenge with significant implications for quantum computing, clock synchronisation, secure communications, and quantum sensing. In a quantum network, photons interact with…
In the pursuit of designing safer and more efficient energy-absorbing structures, engineers must tackle the challenge of improving crush performance while balancing multiple conflicting objectives, such as maximising energy absorption and…
A number of coupling strategies are presented for stochastically modeled biochemical processes with time-dependent parameters. In particular, the stacked coupling is introduced and is shown via a number of examples to provide an…
We address several questions in reduced versus extended networks via the elimination or addition of intermediate complexes in the framework of chemical reaction networks with mass-action kinetics. We clarify and extend advances in the…
Biomolecular condensates help organize the cell cytoplasm and nucleoplasm into spatial compartments with different chemical compositions. A key feature of such compositional patterning is the local enrichment of enzymatically active…
Various kinetic Monte Carlo algorithms become inefficient when some of the population sizes in a system are large, which gives rise to a large number of reaction events per unit time. Here, we present a new acceleration algorithm based on…
The widespread popularity of replica exchange and expanded ensemble algorithms for simulating complex molecular systems in chemistry and biophysics has generated much interest in enhancing phase space mixing of these protocols, thus…
A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is proposed that is able to work with a very large number of collective coordinates. Acceleration of the dynamics is achieved by constructing a bias…
The paper is devoted to further development of the new approach in equilibrium statistical mechanics the basis of which was worked out in a series of articles by the author. The approach proceeds on the use of a hierarchy of equations for…
The existing literature on stochastic simulation of chemical reaction networks has a tendency to move as quickly as possible to the abstract formulation of the stochastic dynamics in terms of probabilities based on the concept of the…