Related papers: Conformational selection and induced changes along…
Predicting enzyme kinetic parameters quantifies how efficiently an enzyme catalyzes a specific substrate under defined biochemical conditions. Canonical parameters such as the turnover number ($k_\text{cat}$), Michaelis constant…
The escalating demand for high-speed and high-precision machining in machine tool feed system has brought to the forefront the challenge of its design method. Currently, existing methodologies struggle to ascertain compliance with dynamic…
We perform stability analysis of a kinetic bacterial chemotaxis model of bacterial self-organization, assuming that bacteria respond sharply to chemical signals. The resulting discontinuous tumbling kernel represents the key challenge for…
Understanding the condensed-phase behavior of chiral molecules is important in biology, as well as in a range of technological applications, such as the manufacture of pharmaceuticals. Here, we use molecular dynamics simulations to study a…
Cellular responses often require the fast activation or repression of specific genes, which depends on Transcription Factors (TFs) that have to quickly find the promoters of these genes within a large genome. Transcription Factors (TFs)…
The transition to sustainable green hydrogen production demands innovative electrocatalyst design strategies that can overcome current technological limitations. This study introduces a comprehensive data-driven approach to predicting and…
While recent advances in AI have transformed protein structure prediction, protein function is also strongly influenced by the thermodynamic and kinetic features encoded in its underlying free-energy surface. Here, we propose a…
We consider mechanically-induced pattern formation within the framework of a growing, planar, elastic rod attached to an elastic foundation. Through a combination of weakly nonlinear analysis and numerical methods, we identify how the shape…
Metal-organic frameworks (MOFs) provide a versatile and tailorable material platform that embody many desirable attributes for photocatalytic water-splitting. The approach taken in this study was to use Density Functional Theory (DFT) to…
Evolutionary trajectories and phenotypic states available to cell populations are ultimately dictated by intermolecular interactions between DNA, RNA, proteins, and other molecular species. Here we study how evolution of gene regulation in…
A growing number of experimental evidence shows that it is general for a ligand binding protein to have a potential for allosteric regulation and for further evolution. In addition, such proteins generically change their conformation upon…
Nanoscale molecular transport plays a crucial role in regulating mass diffusion and responsiveness in condensed matter systems. In soft porous crystals, in particular, adsorption of guest molecules induces host framework deformation and…
Non-native conformations drive protein misfolding diseases, complicate bioengineering efforts, and fuel molecular evolution. No current experimental technique is well-suited for elucidating them and their phenotypic effects. Especially…
Many animal cells change their shape depending on the stiffness of the substrate on which they are cultured: they assume small, rounded shapes in soft ECMs, they elongate within stiffer ECMs, and flatten out on hard substrates. Cells tend…
Epigenetic modifications of histones crucially affect the eukaryotic gene activity, while the epigenetic histone state is largely determined by the binding of specific factors such as the transcription factors (TFs) to DNA. Here, the way…
During the past century, biologists and mathematicians investigated two mechanisms underlying bacteria motion: the run phase during which bacteria move in straight lines and the tumble phase in which they change their orientation. When…
We construct a new hydrodynamic framework describing plastic deformations in electronic crystals. The framework accounts for pinning, phase, and momentum relaxation effects due to translational disorder, diffusion due to the presence of…
A morphogenic protein known as Dorsal patterns the embryonic dorsoventral body axis of Drosophila by binding to transcriptional enhancers across the genome. Each such enhancer activates a neighboring gene at a unique threshold concentration…
Understanding the role of elastic strain in modifying catalytic reaction rates is crucial for catalyst design, but experimentally, this effect is often coupled with a ligand effect. To isolate the strain effect, we have investigated the…
Although the classical density functional theory (DFT) of inhomogeneous fluids was formulated more than four decades ago, its application to broken symmetry phases of molecular systems remained a challenge. Approximate free energy…