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Classical empirical force fields have dominated biomolecular simulation for over 50 years. Although widely used in drug discovery, crystal structure prediction, and biomolecular dynamics, they generally lack the accuracy and transferability…
Multisite covalent modification of proteins is omnipresent in eukaryotic cells. A well-known example is the mitogen-activated protein kinase (MAPK) cascade, where in each layer of the cascade a protein is phosphorylated at two sites. It has…
We theoretically predict and experimentally observe the onset of weak-link physics in the dynamical response of transition edge sensors (TES). We develop a theoretical framework based on a Fokker-Planck description that incorporates both…
The proteins involved in cells' mechanobiological processes have evolved specialized and surprising responses to applied forces. Biochemical transformations that show catch-to-slip switching and force-induced pathway switching serve…
Most tactile actuators create tactile sensations through vibrations or the mechanical and electrochemical formation of bumps. However, tactile sensations of real objects arise from friction which is derived not only from physical…
We report the simultaneous characterization of time- and force-dependent mechanical properties of adherent cells in the physiologically relevant regime of large forces. We used magnetic tweezers to apply forces to magnetic beads bound to…
Motion is an important feature of visual scenes and retinal neuronal circuits selectively signal different motion features. It has been shown that the retina can extrapolate the position of a moving object, thereby compensating sensory…
Conformational barcodes tag functional sites of proteins, and are decoded by interacting molecules transmitting the incoming signal. Conformational barcodes are modified by all co-occurring allosteric events induced by post-translational…
A tethered vesicle, which consists of a cylindrical membrane tube and a spherical vesicle, is produced by a mechanical force that is experimentally imposed by optical tweezers and a micropipette. This tethered vesicle is employed for…
In this paper, we propose a novel concept for engineered molecular communication (MC) systems inspired by animal olfaction. We focus on a multi-user scenario where transmitters employ unique mixtures of different types of signaling…
The sliding friction force exerted by stochastic linkers interacting with a moving filament is calculated. The elastic properties of the substrate on which the linkers are anchored are shown to strongly influence the friction force. In some…
The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can…
The measurement of parameters that describe kinetic processes is important in the study of molecular interactions. It enables a deeper understanding of the physical mechanisms underlying how different biological entities interact with each…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Integrins are allosteric cell adhesion receptors that control many important processes, including cell migration, proliferation, and apoptosis. Ligand binding activates integrins by stabilizing an integrin conformation with separated…
We present a novel formulation for biochemical reaction networks in the context of signal transduction. The model consists of input-output transfer functions, which are derived from differential equations, using stable equilibria. We select…
Plants sense their environment by producing electrical signals which in essence represent changes in underlying physiological processes. These electrical signals, when monitored, show both stochastic and deterministic dynamics. In this…
Traction force microscopy is a method widely used in biophysics and cell biology to determine forces that biological cells apply to their environment. In the experiment, the cells adhere to a soft elastic substrate, which is then deformed…
We consider a theoretical model for membranes with adhesive receptors, or stickers, that are actively switched between two conformational states. In their 'on'-state, the stickers bind to ligands in an apposing membrane, whereas they do not…
The increasing interest in photoactivated proteins as natural replacement of standard inorganic materials in photocells drives to the compared analysis of bacteriorhodopsin and proteorhodopsin, two widely diffused proteins belonging to the…