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We examine fluctuation effects due to the low copy number of proteins involved in pattern-forming dynamics within a bacterium. We focus on a stochastic model of the oscillating MinCDE protein system regulating accurate cell division in E.…
We use molecular dynamics computer simulations to investigate the coupling/decoupling between translational and rotational dynamics in a glass-forming liquid of dumbbells. This is done via a careful analysis of the $\alpha$-relaxation time…
We numerically investigate the collision dynamics and deformation behaviors of double-core compound droplet pairs within confined shear flows using free-energy-based lattice Boltzmann method. While significant research has advanced our…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
Kinetic parameters such as the turnover number ($k_{cat}$) and Michaelis constant ($K_{\mathrm{M}}$) are essential for modelling enzymatic activity but experimental data remains limited in scale and diversity. Previous methods for…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
Incomplete release profiles of protein delivery systems can be caused by unfolding and denaturation of proteins due to protein-biomaterial interactions. This paper investigates the mechanisms causing incomplete release of the wound healing…
Chemically reacting systems exhibiting a repeatable delay period before a visible and sudden change are referred to as clock reactions; they have a long history in education and provide an idealisation of various biochemical and industrial…
E. Coli. dihydrofolate reductase (DHFR) undergoes conformational transitions between the closed (CS) and occluded (OS) states which, respectively, describe whether the active site is closed or occluded by the Met20 loop. A sequence-based…
Production of heat shock proteins are induced when a living cell is exposed to a rise in temperature. The heat shock response of protein DnaK synthesis in E.coli for temperature shifts from temperature T to T plus 7 degrees, respectively to…
We present a kinetic Monte Carlo study of the dynamical response of a Ziff-Gulari-Barshad model for CO oxidation with CO desorption to periodic variation of the CO presure. We use a square-wave periodic pressure variation with parameters…
The analysis of stress response systems in microorganisms can reveal molecular strategies for regulatory control and adaptation. Here, we focus on the Cad module, a subsystem of E. coli's response to acidic stress, which is conditionally…
Increasing interest in sustainable synthesis of ammonia, nitrates, and urea has led to an increase in studies of catalytic conversion between nitrogen-containing compounds using heterogeneous catalysts. Density functional theory (DFT) is…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. We here present a community-driven initiative to address…
The key to understanding a protein's function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structural transitions, conformational flexibility and function of…
Electrocardiography (ECG) signals play a pivotal role in many healthcare applications, especially in at-home monitoring of vital signs. Wearable technologies, which these applications often depend upon, frequently produce low-quality ECG…
We present a theoretical analysis of the dynamic structure factor (DSF) of a liquid at and below the mode coupling critical temperature $T_c$, by developing a self-consistent theoretical treatment which includes the contributions both from…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
Coherence evolution and echo effect of an electron spin, which is coupled inhomogeneously to an interacting one-dimensional finite spin bath via hyperfine-type interaction, is studied using the adaptive time dependent density matrix…