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This contribution proposes the first 3D beam-to-beam interaction model for molecular interactions between curved slender fibers undergoing large deformations. While the general model is not restricted to a specific beam formulation, in the…
Optical microscopy provides rich spatio-temporal information characterizing in vivo molecular motion. However, effective forces and other parameters used to summarize molecular motion change over time in live cells due to latent state…
Accurately predicting complex protein-protein interactions (PPIs) is crucial for decoding biological processes, from cellular functioning to disease mechanisms. However, experimental methods for determining PPIs are computationally…
Chemical reactions are usually studied under the assumption that both substrates and catalysts are well mixed (WM) throughout the system. Although this is often applicable to test-tube experimental conditions, it is not realistic in…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
Using computer simulations, we identify the mechanisms causing aggregation and structural arrest of colloidal suspensions interacting with a short-ranged attraction at moderate and high densities. Two different non-ergodicity transitions…
The ion-activated patchy particle model is an important theoretical framework to investigate the phase behaviour of globular proteins in the presence of multivalent ions. In this work, we study and highlight the influence of patch…
Under appropriate conditions, mixtures of cationic and neutral lipids and DNA in water condense into complexes in which DNA strands form local 2D smectic lattices intercalated between lipid bilayer membranes in a lamellar stack. These…
In this work we determine a process-level Large Deviation Principle (LDP) for a model of interacting particles indexed by a lattice $\mathbb{Z}^d$. The connections are random, sparse and unscaled, so that the system converges in the large…
The shapes of liquid polystyrene (PS) droplets on viscoelastic polydimethylsiloxane (PDMS) substrates are investigated experimentally using atomic force microscopy for a range of droplet sizes and substrate elasticities. These shapes, which…
Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP…
We derive a mode-coupling theory for the slow dynamics of fluids confined in disordered porous media represented by spherical particles randomly placed in space. Its equations display the usual nonlinear structure met in this theoretical…
The apparent stochasticity of in-vivo neural circuits has long been hypothesized to represent a signature of ongoing stochastic inference in the brain. More recently, a theoretical framework for neural sampling has been proposed, which…
Experimental research has shown that the brain's fast electrochemical dynamics, or neurodynamics (ND), is strongly stochastic, chaotic, and instanton (neuroavalanche)-dominated. It is also partly scale-invariant which has been loosely…
Rhythmic activity has been associated with a wide range of cognitive processes. Previous studies have shown that spike-timing-dependent plasticity can facilitate the transfer of rhythmic activity downstream the information processing…
Biomolecular condensates form on timescales of seconds in cells upon environmental or compositional changes. Condensate formation is thus argued to act as a mechanism for sensing such changes and quickly initiating downstream processes,…
Low-density networks of molecules or colloids are formed at low temperatures when the interparticle interactions are valence limited. Prototypical examples are networks of patchy particles, where the limited valence results from highly…
Driven diffusive systems such as the zero-range process (ZRP) and the pair-factorized steady states (PFSS) stochastic transport process are versatile tools that lend themselves to the study of transport phenomena on a generic level. While…
The quest for highly efficient cognitive computing has led to extensive research interest for the field of neuromorphic computing. Neuromorphic computing aims to mimic the behavior of biological neurons and synapses using solid-state…
Recent biological experimental findings have shown that synaptic plasticity depends on the relative timing of pre- and post-synaptic spikes and this is called spike-timing-dependent plasticity (STDP). Many authors have claimed that a…