Related papers: Entropy-driven phase behaviour of all-DNA associat…
The emergence of longer information-carrying and functional nucleotide polymers from random short strands was a major stepping stone at the dawn of life. But the formation of those polymers under temperature oscillation required some form…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
By taking into account base-base stacking interactions we improve the Generalized Model of Polypeptide Chain (GMPC). Based on a one-dimensional Potts-like model with many-particle interactions, the GMPC describes the helix-coil transition…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…
We study the electronic properties of coupled parallel Polyyne chains in a couple of symmetric stacking arrangements, namely the AA stacking and the stacking AB, with the single and triple carbon bonds of one chain aligned (AA) and…
We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with…
Atom connecting positions(ACPs) are positions where an atom is connecting to another one or a few atoms, which is needed when constructing final state used in chain-of-state(CoS) methods for transition state(TS) locating and minimum energy…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
In this paper, we present a study of supercooled liquids interacting with the Lennard Jones (LJ) potential and the corresponding purely repulsive (Weeks-Chandler-Andersen or WCA) potential, over a range of densities and temperatures, in…
Biological polymers, such as intrinsically disordered proteins, play a central role in cellular biology, including mediating phase separation and controlling activity of biological condensates. The physical properties and functions of…
A collection of rings made of active Brownian particles (ABPs) for different packing fractions and activities is investigated using computer simulations. We show that active rings display an emergent dynamic clustering instead of the…
Predicting favorable protein-peptide binding events remains a central challenge in biophysics, with continued uncertainty surrounding how nonlocal effects shape the global energy landscape. Here, we introduce peripheral surface information…
We study a generic model of self-assembling chains which can branch and form networks with branching points (junctions) of arbitrary functionality. The physical realizations include physical gels, wormlike micells, dipolar fluids and…
The specificity and thermal reversibility of DNA interactions have enabled the self-assembly of crystal structures, self-replicating materials and colloidal molecules. Grafting DNA onto liquid interfaces of emulsions leads to exciting new…
We consider the statistical mechanics of a system of topologically linked polymers, such as for instance a dense solution of polymer rings. If the possible topological states of the system are distinguished using the Gauss linking number as…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
Understanding stochastic thermodynamics of active Brownian particles (ABPs) system has been an important topic in very recent years. In this article we study a general model of active Brownian particle systems by introducing a…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…
Solid-state nanopore and nanopipette sensors are powerful devices for the detection, quantification and structural analysis of biopolymers such as DNA and proteins, especially in carrier-enhanced resistive-pulse sensing. However, hundreds…
When two or more atoms bind to a solid surface, the substrate can mediate an interaction between them. In this paper, we use density-functional theory to quantify the substrate-mediated pair interaction between two adatoms on a…