Related papers: Electrostatic Binding and Hydrophobic Collapse of …
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
We use first principles methods to study static and dynamical mechanical properties of the ferroelectric polymer Poly(vinylidene fluoride) (PVDF) and its copolymer with trifluoro ethylene (TrFE). We use density functional theory [within the…
Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for the coarse grained…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
A series of well-defined hydrophilic and hydrophobic polyelectrolytes of various chain lengths $N$ and effective charge fractions $f_{eff}$ have been adsorbed onto oppositely charged solid surfaces immersed in aqueous solutions. \emph{In…
The possibility for proteins to aggregate in different superstructures, i.e. large-scale polymorphism, has been widely observed, but an understanding of the physico-chemical mechanisms behind it is still out of reach. Here we present a…
Using computer simulations of over 100,000 atoms, the mechanism for the hydrophobic collapse of an idealized hydrated chain is obtained. This is done by coarse-graining the atomistic water molecule positions over 129,000 collective…
Photodynamically active fibres (PAFs) are a novel class of stimulus-sensitive systems capable of triggering antibiotic-free antibacterial effect on-demand when exposed to light. Despite their relevance in infection control, however, the…
Amide resonance is found to be sensitive to electrostatic field with component parallel or antiparallel to the amide C-N bond, an effect we refer to here as EVPR-CN. EVPR-CN is linear and without threshold in the biologically plausible…
We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics (MD) simulations are suggested by single-molecule studies of protein-DNA…
Similarly-charged polyelectrolytes are known to attract each other and aggregate into bundles when the charge density of the polymers exceeds a critical value that depends on the valency of the counterions. The dynamics of aggregation of…
The Exact Factorization (XF) of molecular wavefunctions can be viewed as an 'electronic wavepacket' framework for quantum dynamics. It is an appealing alternative to the conventional non-adiabatic dynamics, unfolding in the space of coupled…
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…
Aggregation of two oppositely charged colloids in salty water is studied. We focus on the role of Coulomb interaction in strongly asymmetric systems in which the charge and size of one colloid is much larger than the other one. In the…
We study the effective interaction mediated by strongly coupled Coulomb fluids between dielectric surfaces carrying quenched, random monopolar charges with equal mean and variance, both when the Coulomb fluid consists only of mobile…
Optical tweezers are employed to measure the forces of interaction within a single pair of DNA-grafted colloids in dependence of the molecular weight of the DNA-chains, and the concentration and valence of the surrounding ionic medium. The…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
The combination of two techniques (Small Angle X-ray Scattering and Atomic Force Microscopy) has allowed us to measure in reciprocal and real space the correlation length $\xi$ of salt-free aqueous solutions of highly charged hydrophobic…
Autonomous electrolyte discovery demands a computational engine that satisfies a critical trilemma: it must be fast enough for high-throughput screening, accurate enough for quantitative property prediction, and calibratable enough for…