Related papers: Ultrasensitivity and sharp threshold theorems for …
Using a statistical mechanical model and numerical simulations, we provide the design principle for the bridging strength ($\xi$) and linker density ($\rho$) dependent superselectivity in linker-mediated multivalent nanoparticle adsorption.…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary…
One of the fundamental challenges in drawing causal inferences from observational studies is that the assumption of no unmeasured confounding is not testable from observed data. Therefore, assessing sensitivity to this assumption's…
By use of the conservation laws a four-site Hubbard model coupled to a particle bath within an external magnetic field in z-direction was diagonalized. The analytical dependence of both the eigenvalues and the eigenstates on the interaction…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
Multivalent particles bind to targets via many independent ligand-receptor bonding interactions. This microscopic design spans length scales in both synthetic and biological systems. Classic examples include interactions between cells,…
Observing a load process above high thresholds, modeling it as a pulse process with random occurrence times and magnitudes, and extrapolating life-time maximum or design loads from the data is a common task in structural reliability…
Searching for reaction pathways describing rare events in large systems presents a long-standing challenge in chemistry and physics. Incorrectly computed reaction pathways result in the degeneracy of microscopic configurations and inability…
Many biological molecular motors and machines are driven by chemical reactions that occur in specific catalytic sites. We study whether the arrival of molecules to such an active site can be accelerated by the presence of a nearby inactive…
A new type of cooperativity termed temporal cooperativity [Biophys. Chem. 105 585-593 (2003), Annu. Rev. Phys. Chem. 58 113-142 (2007)], emerges in the signal transduction module of phosphorylation-dephosphorylation cycle (PdPC). It…
We study the mechanics of a reversible decohesion (unzipping) of an elastic layer subjected to quasi-static end-point loading. At the micro level the system is simulated by an elastic chain of particles interacting with a rigid foundation…
We demonstrate how the collective response of $N$ globally coupled bistable elements can strongly reflect the presence of very few non-identical elements in a large array of otherwise identical elements. Counter-intuitively, when there are…
It has recently been shown that structural conditions on the reaction network, rather than a 'fine-tuning' of system parameters, often suffice to impart 'absolute concentration robustness' on a wide class of biologically relevant,…
Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the…
One of the most remarkable results of quantum mechanics is the fact that many-body quantum systems may exhibit phase transitions even at zero temperature. Quantum fluctuations, deeply rooted in Heisenberg's uncertainty principle, and not…
In this work, we consider systems that are subjected to intermittent instabilities due to external stochastic excitation. These intermittent instabilities, though rare, have a large impact on the probabilistic response of the system and…
In molecular dynamics, statistics of transitions, such as the mean transition time, are macroscopic observables which provide important dynamical information on the underlying microscopic stochastic process. A direct estimation using…
This paper studies the sensitivity analysis of mass-action systems against their diffusion approximations, particularly the dependence on population sizes. As a continuous time Markov chain, a mass-action system can be described by a…
Molecular systems containing donor-bridge-acceptor sites or molecular antennas constitute promising candidates for organic photovoltaic device implementation. Photo-induced electron transfer in multi-chromophore molecular systems is defined…