Related papers: Simulating Mono-and Multi-Protein Phosphorylation …
We review theoretical approaches, experiments and numerical simulations that have been recently proposed to investigate the folding problem in single-domain proteins. From a theoretical point of view, we emphasize the energy landscape…
Nanoscale and microscale confinement of biopolymers naturally occurs in cells and has been recently achieved in artificial structures designed for nanotechnological applications. Here, we present an extensive theoretical investigation of…
The multifractal detrended fluctuation analysis of time series is able to reveal the presence of long-range correlations and, at the same time, to characterize the self-similarity of the series. The rich information derivable from the…
Interparticle interactions and bulk properties of colloidal suspensions can be substantially modified by addition of nanoparticles. Extreme asymmetries in size and charge between colloidal particles and nanoparticles present severe…
We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can…
Multiplicity fluctuations of intermediate-mass fragments are studied with the percolation model. It is shown that super-Poissonian fluctuations occur near the percolation transition and that this behavior is associated with the…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
Polymer-coated pores play a crucial role in nucleo-cytoplasmic transport and in a number of biomimetic and nanotechnological applications. Here we present Monte Carlo and Density Functional Theory approaches to identify different collective…
Beerenwinkel et al.(2007) suggested studying fitness landscapes via regular subdivisions of convex polytopes. Building on their approach we propose cluster partitions and cluster filtrations of fitness landscapes as a new mathematical tool.…
Understanding polymorph selection in atomic and molecular systems and its control through thermodynamic conditions and external factors (such as seed characteristics) is fundamental to the design of targeted materials and holds great…
Protein phosphorylation involves the reversible modification of a protein (substrate) residue by another protein (kinase). Liquid chromatography-mass spectrometry studies are rapidly generating massive protein phosphorylation datasets…
The assembly of banana-shaped rodlike proteins on membranes, and the associated membrane shape transformations, are investigated by analytical theory and coarse-grained simulations. The membrane-mediated interactions between two…
Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells,…
The increasing utilization of charged particle beams for therapeutic purposes requires designing novel detector systems which shall be capable of assessing radiation quality for a diversity of ion species. It is shown that the pattern of…
Motor proteins drive persistent motion and self-organisation of cytoskeletal filaments. However, state-of-the-art microscopy techniques and continuum modelling approaches focus on large length and time scales. Here, we perform…
The simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…
Proteins are intricate molecular machines whose complexity arises from the heterogeneity of the amino acid building blocks and their dynamic network of many-body interactions. These nanomachines gain function when put in the context of a…