Related papers: Ultrasensitivity and sharp threshold theorems for …
Receptor-ligand interactions are essential for biological function and their binding strength is commonly explained in terms of static lock-and-key models based on molecular complementarity. However, detailed information of the full…
We study correlated switchings of superconducting nanobridge probed with train of current pulses. For pulses with low repetition rate each pulse transits the superconducting bridge to normal state with probability $P$ independent of the…
We examine the behavior of entanglement entropy of a subsystem $A$ in a fully backreacted holographic model of a $1+1$ dimensional $p$ wave superconductor across the phase transition. For a given temperature, the system goes to a…
Strongly correlated solids are extremely complex and fascinating quantum systems, where new states continue to emerge, especially when interaction with light triggers interplay between them. In this interplay, sub-laser-cycle electron…
System with strong photon-phonon interaction and optomechanical instability are perspective for generation of coherent phonons and photons. Typically, above the threshold of optomechanical instability, the photon intensity increases…
From systematic ab initio calculations of the alloy system Mg_{1-x}Al_{x}B_2, we find a strong tendency for the formation of a superstructure characterized by Al-rich layers. We also present a simple model, based on calculated energies and…
We consider the problem of estimating parameter sensitivity for Markovian models of reaction networks. Sensitivity values measure the responsiveness of an output to the model parameters. They help in analyzing the network, understanding its…
Building on the recently derived inhomogeneous mode-coupling theory, we extend the generalised mode-coupling theory of supercooled liquids to inhomogeneous environments. This provides a first-principles-based, systematic and rigorous way of…
Sensitivity analysis of multibody systems computes the derivatives of general cost functions that depend on the system solution with respect to parameters or initial conditions. This work develops adjoint sensitivity analysis for hybrid…
We study the entanglement entropy and entanglement spectrum of the paradigmatic Bose-Hubbard model, describing strongly correlated bosons on a lattice. The use of a controlled approximation - the slave-boson approach - allows us to study…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
We investigate the collisional stability of magnetically trapped ultracold molecules, taking into account the influence of magnetic fields. We compute elastic and spin-state-changing inelastic rate constants for collisions of the prototype…
In this paper we study a simple stochastic version of the Hopfield-Ninio kinetic proofreading model. The model is characterized by means of two parameters, the unbinding time, which depends on the binding energy between a ligand and a…
Biochemical reaction models describing subcellular processes generally come with a large uncertainty. To be able to account for this during the modeling process, we have developed the R-package UQSA, performing uncertainty quantification…
We present an adjoint sensitivity method for hybrid discrete -- continuous systems, extending previously published forward sensitivity methods. We treat ordinary differential equations and differential-algebraic equations of index up to two…
Contagion processes have been proven to fundamentally depend on the structural properties of the interaction networks conveying them. Many real networked systems are characterized by clustered substructures representing either collections…
Predicting accurate protein-ligand binding affinity is important in drug discovery but remains a challenge even with computationally expensive biophysics-based energy scoring methods and state-of-the-art deep learning approaches. Despite…
We establish well-posedness results for systems of a finite number of stochastic particles driven by independent Brownian motions and subject to a strongly singular drift induced by a Lennard-Jones interaction. In addition to the pairwise…
From a rigorous multichannel quantum-defect formulation of bimolecular processes, we derive a fully quantal and analytic model for the total rate of exoergic bimolecular reactions and/or inelastic processes that is applicable over a wide…
Protein-ligand interactions are crucial for a wide range of physiological processes. Many cellular functions result in these non-covalent `bonds' being mechanically strained, and this can be integral to proper cellular function. Broadly,…