Related papers: Dissecting Ubiquitin Folding Using the Self-Organi…
We establish an experimental method for a detailed investigation of inelastic collisional properties between ytterbium (Yb) in the metastable ${}^3\mathrm{P}_2$ state and ground state lithium (Li). By combining an optical lattice and a…
We present force-clamp data on the collapse of ubiquitin polyproteins in response to a quench in the force. These nonequilibrium trajectories are analyzed using a general method based on a diffusive assumption of the end-to-end length to…
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
Recent demonstrations of extraordinary stabilization of proteins in mobile protic [1] and aprotic [2] ionic liquid solutions at ambient temperatures have raised hopes of new biopreservation and drug transportation technologies. Here we…
The structural and dynamical properties of ultra-soft colloids - star polymers - exposed to a uniform external force field are analyzed applying the multiparticle collision dynamics approach, a hybrid coarse-grain mesoscale simulation…
Finite systems of bosons and/or fermions described by the Hubbard model can be realized using ultracold atoms confined in optical lattices. The ground states of these systems often exhibit a coexistence of compressible superfluid and…
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…
Non-Hermitian dynamics in open systems can give rise to a variety of fascinating non-equilibrium phenomena, ranging from symmetry-breaking transitions to directional energy flow. Parity-time (PT) symmetry breaking determines the occurrence…
The high-pressure behaviour of PbS was investigated by angular dispersive X-ray powder diffraction up to pressures of 6.8 GPa. Experiments were accompanied by first principles calculations at the density functional theory level. By…
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
Biopolymer self-assembly pathways are central to biological activity, but are complicated by the ability of the monomeric subunits of biopolymers to adopt different conformational states. As a result, biopolymer nucleation often involves a…
We implement the replica exchange molecular dynamics algorithm to study the interactions of a model peptide (WALP-16) with an explicitly represented DPPC membrane bilayer. We observe the spontaneous, unbiased insertion of WALP-16 into the…
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
We propose a four-component molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse-graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are…
Nucleation phenomena commonly observed in our every day life are of fundamental, technological and societal importance in many areas, but some of their most intimate mechanisms remain however to be unravelled. Crystal nucleation, the early…
This theoretical study concerns a pH oscillator based on the urea-urease reaction confined to giant lipid vesicles. Under suitable conditions, differential transport of urea and hydrogen ion across the unilamellar vesicle membrane…
A system consisting of a doubly clamped beam with an attached body (slider) free to move along the beam has been studied recently by multiple research groups. Under harmonic base excitation, the system has the capacity to passively adapt…