相关论文: Universality of fold-encoded localized vibrations …

Many biologically important ligands of proteins are large, flexible, and often charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods…

We put forward a general field theory for membranes with embedded activators and analyse their critical properties using renormalization group techniques. Depending on the membrane-activator coupling, we find a crossover between acoustic…

Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…

Site-specific transcription factors (TFs) bind to their target sites on the DNA, where they regulate the rate at which genes are transcribed. Bacterial TFs undergo facilitated diffusion (a combination of 3D diffusion around and 1D random…

The surface a thin-film is attached to and the surrounding monolayer causes geometrical confinement of a interrogated molecule; we look at the base case of a SC$_{18}H_{37}$ in a SC$_{18}H_{37}$ monolayer on Au[111]. Normal mode analysis…

The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can…

Surfaces are at the frontier of every known solid. They provide versatile supports for functional nanostructures and mediate essential physicochemical processes. Being intimately related with 2D materials, interfaces and atomically thin…

Evolution in its course found a variety of solutions to the same optimisation problem. The advent of high-throughput genomic sequencing has made available extensive data from which, in principle, one can infer the underlying structure on…

Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…

The regulation of various cellular processes heavily relies on the protein complexes within a living cell, necessitating a comprehensive understanding of their three-dimensional structures to elucidate the underlying mechanisms. While…

Hydrogen peroxide oxidises cysteine residues to control protein function, yet bulk rate constants predict hours for changes that occur in cells in seconds. Here, this work shows that local electromagnetic fields (EMFs), ubiquitous in…

Currently, biological signaling is envisaged as a combination of activation and movement, triggered by local molecular interactions and molecular diffusion, respectively. However, we here suggest, that other fundamental physical mechanisms…

Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…

Spatiotemporal pattern formation in a product-activated enzymic reaction at high enzyme concentrations is investigated. Stochastic simulations show that catalytic turnover cycles of individual enzymes can become coherent and that complex…

A novel mechanism of reaction-induced active molecular motion, not involving any kind of self-propulsion, is proposed and analyzed. Because of the momentum exchange with the surrounding solvent, conformational transitions in…

Strongly interacting electrons in layered materials give rise to a plethora of emergent phenomena, such as unconventional superconductivity. heavy fermions, and spin textures with non-trivial topology. Similar effects can also be observed…

The detection of vibrational excitations of individual molecules on surfaces by scanning tunneling spectroscopy does not obey strict selection rules but rather propensity rules. The experimental verification of these is challenging because…

Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…

At room temperature, low frequency vibrations at far-infrared frequencies are thermally excited ($k_B T > h \nu$) and not restricted to harmonic fluctuations around a single potential energy minimum. For folded proteins, these intrinsically…

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…