Related papers: Frustration, dynamics and catalysis
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
We present a new kinetic equation for cell migration driven by mechanical interactions with the substrate, an effect not previously captured in kinetic models, and essential for explaining observed collective behaviors such as those in…
Gene regulatory dynamics is governed by molecular processes and therefore exhibits an inherent stochasticity. However, for the survival of an organism it is a strict necessity that this intrinsic noise does not prevent robust functioning of…
Proteins evolve through complex sequence spaces, with fitness landscapes serving as a conceptual framework that links sequence to function. Fitness landscapes can be smooth, where multiple similarly accessible evolutionary paths are…
Synchronization of activity among myocytes constituting vital organs, e.g., the heart, is crucial for physiological functions. Self-organized coordination in such heterogeneous ensemble of excitable and oscillatory cells is therefore of…
Pulsatory activity patterns, driven by mechanochemical feedback, are prevalent in many biological systems. Here we present a theoretical framework to elucidate the mechanical origin and regulation of pulsatile activity patterns within…
We analyse the mechanism of enzyme-substrate catalysis from the perspective of minimizing the load on the enzymes through sequestration, whilst maintaining at least a minimum reaction flux. In particular, we ask: which binding free energies…
All life, including cells and artificial protocells, must integrate diverse molecules into a single unit in order to reproduce. Despite expected pressure to evolve a simple system with the fastest replication speed, the mechanism by which…
Geometric frustration arises whenever the constituents of a physical assembly locally favor an arrangement that cannot be realized globally. Recently, such frustrated assemblies were shown to exhibit filamentation, size limitation, large…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
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…
How do single cell fate decisions induced by activation of key signaling proteins above threshold concentrations within a time interval are affected by stochastic fluctuations in biochemical reactions? We address this question using minimal…
The process of evolution by natural selection leads to phenotypes of increasing fitness. For cellular chemical reaction networks, this means optimising a variety of fitness functions such as robustness, precision, or sensitivity to external…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
Mechanical forces influence the dynamics of growing tissues. Computer simulations are employed to study the importance of interfacial effects in tissue competition. It was speculated that mechanical pressure determines the competition,…
Many biological systems perform close to their physical limits, but promoting this optimality to a general principle seems to require implausibly fine tuning of parameters. Using examples from a wide range of systems, we show that this…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular…
Besides being a fascinating class of new materials, magnetic molecules provide the opportunity to study concepts of condensed matter physics in zero dimensions. This contribution will exemplify the impact of molecular magnetism on concepts…