Related papers: Cooperative Function with Thermal Fluctuations in …
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…
Thermal fluctuations constantly and evenly excite all vibrational modes in an equilibrium crystal. As the temperature rises, these fluctuations promote the formation of defects and eventually melting. In active solids, the self-propulsion…
We introduce a multi-species network model which describes the resistance fluctuations of a resistor in a non-equilibrium stationary state. More precisely, a thin resistor characterized by a 1/f^alpha resistance noise is described as a…
We study the elastic properties of a two-dimensional fluctuating surface whose area density is allowed to deviate from its optimal (Schulman) value. The behavior of such a surface is determined by an interplay between the area-dependent…
We aim to identify the control principles governing the adaptable formation of non-equilibrium structures in actomyosin networks. We build a phenomenological model and predict that biasing the energy dissipated by molecular motors should…
Allosteric effects are often underlying the activity of proteins and elucidating generic design aspects and functional principles which are unique to allosteric phenomena represents a major challenge. Here an approach which consists in the…
We develop a transferable machine learning model which predicts structural relaxation from amorphous supercooled liquid structures. The trained networks are able to predict dynamic heterogeneity across a broad range of temperatures and time…
We simulate the electrical properties of a device realized by a G protein coupled receptor (GPCR), embedded in its membrane and in contact with two metallic electrodes through which an external voltage is applied. To this purpose, recently,…
Biological membranes are elastic media in which the presence of a transmembrane protein leads to local bilayer deformation. The energetics of deformation allow two membrane proteins in close proximity to influence each other's equilibrium…
Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to…
Thermodynamic bulk measurements of binding reactions critically rely on the validity of the law of mass action and the assumption of a dilute solution. Yet important biological systems such as allosteric ligand-receptor binding,…
We introduce an approach to partitioning networks into communities that not only determines the best community structure, but also provides a range of characterization techniques to assess how significant that structure is. We study the…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
The fracture and severing of polymer chains plays a critical role in the failure of fibrous materials and the regulated turnover of intracellular filaments. Using continuum wormlike chain models, we investigate the fracture of semiflexible…
We study the elasticity of cross-linked networks of thermally fluctuating stiff polymers. As compared to their purely mechanical counterparts, it is shown that these thermal networks have a qualitatively different elastic response. By…
Generative models of complex systems often require post-hoc parameter adjustments to produce useful outputs. For example, energy-based models for protein design are sampled at an artificially low ''temperature'' to generate novel,…
Mechanical algesia is an important process for the preservation of living organisms, allowing potentially life-saving reflexes or decisions when given body parts are stressed. Yet, its various underlying mechanisms remain to be fully…
When engineering microscopic machines, increasing efficiency can often come at a price of reduced reliability due to the impact of stochastic fluctuations. Here we develop a general method for performing multi-objective optimisation of…
The zero-temperature XX chain is studied with emphasis on the properties of a block of $L$ spins inside the chain. We investigate the quantum fluctuations resulting from the entanglement of the block with the rest of the chain using…
Symmetry-breaking is pivotal for controlling ferroelectric, ferroelastic and/or ferromagnetic functions of materials, which enables applications in sensors, memories, transducers or actuators. Commonly, ferroic phases emerge from descending…