相关论文: Molecular Spiders in One Dimension

For molecular dynamics simulations of hard particles, we define dynamic neighbors as the distinct particles that collide with a given reference one during a specific time interval. This definition allows us to determine the distribution of…

Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…

How the very first nervous systems evolved remains a fundamental open question. Molecular and genomic techniques have revolutionized our knowledge of the molecular ingredients behind this transition but not yet provided a clear picture of…

We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…

Our understanding of the neural basis of locomotor behavior can be informed by careful quantification of animal movement. Classical descriptions of legged locomotion have defined discrete locomotor gaits, characterized by distinct patterns…

Single-chain nanoparticles (SCNPs) are a new class of macromolecular objects, synthesized through purely intramolecular cross-linking of single polymer chains. We use a multi-scale hydrodynamics simulation approach to study, for the first…

In this work we address a novel feature of spreading dynamics of tiny liquid droplets on solid surfaces, namely the case where the ends of the molecules feel different interactions to the surface. We consider a simple model of dimers and…

We consider networks made of parallel lanes along which particles hop according to driven diffusive dynamics. The particles also hop transversely from lane to lane, hence indirectly coupling their longitudinal dynamics. We present a general…

There is increasing evidence that mammalian cells not only crawl on substrates but can also swim in fluids. To elucidate the mechanisms of the onset of motility of cells in suspension, a model which couples actin and myosin kinetics to…

Surviving in a diverse environment requires corresponding organism responses. At the cellular level, such adjustment relies on the transcription factors (TFs) which must rapidly find their target sequences amidst a vast amount of…

The chemical step is an elementary pattern in chemically heterogeneous substrates, featuring two regions of different wettability separated by a sharp border. Within the framework of lubrication theory, we investigate droplet motion and the…

Although commonly associated with limbless animals like snakes and fish, multi-legged organisms like centipedes also utilize undulatory locomotion. Whether these undulations are actively reinforced or resisted by the axial musculature…

Proteinoids, or thermal proteins, are inorganic entities formed by heating amino acids to their melting point and commencing polymerisation to form polymeric chains. Typically, their diameters range from 10 to 100 micron. Some amino acids…

A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…

Legged machines are becoming increasingly agile and adaptive but they have so far lacked the morphological diversity of legged animals, which have been rearranged and reshaped to fill millions of niches. Unlike their biological…

Single-molecule fluorescence imaging of adsorption onto initially-bare surfaces shows that polymer chains need not localize immediately after arrival. In a system optimized to present limited adsorption sites (quartz surface to which…

A contact map is a simple representation of the structure of proteins and other chain-like macromolecules. This representation is quite amenable to numerical studies of folding. We show that the number of contact maps corresponding to the…

Distance matrices are matrices whose elements are the relative distances between points located on a certain manifold. In all cases considered here all their eigenvalues except one are non-positive. When the points are uncorrelated and…

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the…

The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understanding the self-assembly and replication of this structure are…